TL;DR Mana is converted into Ninki for Jutsus. Engaging in either physical rotation or Jutsu rotation, the Ninja cannot be greedy even in a very good rotational phase, as they must weigh between continuing but over-exerting themselves in one rotational phase, to preparation for a well-setup, sustainable, next-rotational phase. Combo-logic and flow is to be central to Jutsu combo design. Bunshin and Hellfrog medium is to be designed innately to their respective rotational phases, and the overall thematic feel of the Ninja combat is to be defined by the term "dream within a dream".


Below is unorganized rambling completely unrelated to the above paragraph.
They will obviously be amateurish and SE will obviously do a better job, but this is just what I though when prompted with Ninja class design from my own perspective and experience.

1. Thematic "transformation of resources into combat utility"

Ninja would be a "melee magic caster", a rather unique class. That supposedly brings to mind a battle-mage, but we have Paladins for that, and they are a tank. (which brings up a sub-point, classes in this game are too rigidly defined by their roles, and the utility demanded from thus) Ninjas will have to follow a different logic in their thematic design.

I personally do not think this could be done without utilizing the 'Mana' resource, which magic casters revolve around. Currently Ninjas don't really use mana. And I think this is an opportunity wasted.

Because via the transformation of Mana into combat utility, players engage in immersion. Now of course Ninjas don't actually have "mana" in the mage sense, nor should their interaction with their Mana function in the same flow process as a BLM. Which brings up to Ninki. Mana of a ninja should, via some rotation, transform into "Ninki", which is then used for NinJutsus. It should feel as satisfying as charging up, or reloading ammunition to be fired.

It should be 1. thematic to the class and 2. a rewarding loop. For instance, in the popular anime Naruto, the Ninjas are always engaged in absolute exertion. While we do have players yelping in their character's voice-acting now and then when they use skills, what I have in mind is more ... "symbolic", as in straightforwardly, the Ninja does the bits of physical combat, paired with tricks and jutsus, then exerts themselves to use large-scale ultimate Jutsus, then falls back to physical struggling when they are both physically and ... mana-tired. The whole fight should feel like a heroic struggle where you throw all your strength and cunning into it, burning resources with a passion, utilizing force with prejudice.

But this should be rewarding. High-level Ninjas are masters of both magic and magitek, the ultimate spymaster and sensei, who if necessary can do combat regardless of weakness or difficulty. Thus the class should be universally adaptive, yet difficult. Not in the way Monks do it, their thematic setting is more a .. shounen type, straightfoward. Flow. Ninjas are about burst, as are all semi-supportive classes. Using the correct and specific strategy for the situation should reward more than using a general rotation, and achieving a "tactical" perfection in rotation as defining of monks.

Which brings us to the actual rotational flow between Jutsus and Physical combos. Here I would like to insert another piece of theory I think for the Ninja, there should be a "happy-go-lucky" thematic sense, as they start out as 'rogue'. While this sounds very similar to the procs of Bard, which I would like to add I am rather disappointed of this expansion as a class, since SE chose to do away with their thematically defining "songs" and just give them random procs to weave, Ninja procs should straightforwardly be, the Bunshin for physical phase rotation, and the Hellfrog summon for Jutsu phase rotation.

The purpose of transitioning from one phase to the next would then be, how well you can prepare proc chances for Bunshin and your jutsu-summon (cough popular Ninja anime)(scholars be jelly) for the next phase. This will depend on how perfectly you engage in your prior phase rotation, "preparation" and some sort of "weighing-out" between getting more stocked temporal resource and perfect cooldown readiness/alignment, or proceeding with the phase change. One specific "trait choice" will also have to be designed in, similar to Astrologian sect. Or what Machinists had before they got ... very, very streamlined. Or bard songs. You get the idea.

Thus, between two rotations, at least two 'sects', and possibility of some Ninjutsu free-flow combo logic (extra effects depending on which Jutsu you follow up with the prior), there can already by many varying 'overall' combos for the Ninja to chose from, and weigh-out between how they would like to plan out a fight. This is at a strategic level, drawing out for a whole raid fight. So the class would at least not be "stale". However, this alone is not enough.

2. Practicality

To thematically design Ninja into a high-performance, low-drag class that thematically mimics an awesome super-spy or fight-for-life Ninja duels is not enough.
Systemic control points will need to be designed for balance tweaking. It will need to be synced with current raid design philosophy and raid composition philosophy.

So we'll take a look at those. From how I see it, current raids are basically closed, time-synced puzzles with little variation (mechanics are reused). And raid composition philosophy is virtually nonexistent (besides getting a proper head-count composition for mechanics and 5% stats). Between taking away damage types, taking away meaning from resource stats (cough mage ballad and varying mana), even taking away time cooldowns as a resource from rotations (though internal jutsu cooldown timers are not the best example of it), the game is now basically just a rotation-fest. All raid cooldowns are auto-synced to a fight, or not critically mattering even in savage.

There is simply no depth. Or no clear direction that I can see SE are working on towards. They are partitioning every element of this game into separate parts, the open-world grind into Eureka and Diadem, the closed instances (meticulously designed and crafted, to their credit) into raids. This is either a large-scale "control" operation to slim down the game in preparation of some future overhaul and re-fleshing out of the whole game, or a worrying trend that SE is snuffing out any depth and "RPG" like elements (decisions) in this game.

But I am getting sidetracked with my rambling. So how does this factor into Ninja class design?

Because practicality in engaging with game content, is actually part of the immersion. It is not simply " a bunch of adventurers take on a dream two-headed tuna", or that this character, with these skills, adventure through this landscape and story. That is "deep" immersion. There is also "shallow" immersion where you engage with other players, spend your time in this game, and enjoy a funny glamour or spiriting boss theme. Aka. Entertainment efficiency.

A lot of entertainment efficiency can be explained by good game design, fairness, creativity, player agency and choice, etc. It is also polish, uniqueness, good production values. Players expect a modern, highly efficient product to play. SE understands this.

However, it is not, creating single-instance raids where you can literally hop into it in 5 seconds, instead of flying 15 minutes old-school. Because you will waste 15 hours, wiping in it in PF, getting rejected from groups because you are playing an unbalance class aka. Ninja, having to balance gear around cryptic yet in the end, just-get-a-bit-of-each-except-skillspeed because gear ilvl and weapon is all really matters, and SE has you firmly put in your place. The overall system of SE is incomplete, flawed in many places, self-contradicting. So this is all about creating a better system, where good elements can strive, where it can be self-balanced and self-sustainable. This cannot be designed from the bottom-up, it has to be designed with general good practice and future-proof ideals top-down.

SE has to review all their currently available class design tools which they so readily use (do we adjust this with cd? or potency? or proc-chance? or raid-cd sync and utility?) etc. but think above the box, not as engineers and coders, but as designers of a piece of art, symbolic, and a product that demands you treat their users with more variation and less oppressive control compared to general commercial products.

Thus, while I would not prefer to say something sounding like the ideal Ninja class cannot be designed given the current protocols in utilizing of the tools available, to fit into the current system and its philosophy, but the current Ninja class cannot be balanced and redesigned at the same time, without at least preparing for overhead tweaks in the future. Perhaps a larger team is needed. Perhaps more efficient informational work methods will have to be developed to manage something large scale like tweaking a MMO. Perhaps underground botanical vaults are necessary to reduce garden loads on housing districts. Idk. But perhaps a better combat engagement method than the current "mash your rotation via these available buttons on your hotbar which are easily playable even on console yet have little depth" could be envisioned. Idk we're not octopuses we only have two hands. But do we? I've never seen an Octopus play a MMO.

So, need better systems.

3. Dire times

Lack of tanks and healers, is because they are tools.
Healers are mostly nice girls, tanks mostly big male characters.
There is the occasional lion dancer, but I jest.
BTW this has nothing to do with their as tools.

By tools, I mean SE has designed raids into a corner. The most fun is to be had by dps figuring out their strats. Tanks and healers get second priority in gear, but first priority in rezzes (which never happen in a good run), but in the end they are just there for the mechanics. They are tools by which players utilize to gain their weekly loot, though rare ones at that. Other tools, such as cough ranged dps and dancers, or anyone who can't be expected to be near the top end of a dps parse, are semi-tools. And only monks and blm truly play this game.

Did SE desire some classes to be in the spotlight, but some classes interchangeable, even expendable? Dragoons are Bards are no longer BFFs. All raid compositions are more or less the same, there's only the difference between a easy clear and a easier clear. The whole point of the game, whole purpose of even crafting and gathering classes, are in dire straits.

A bad class is demoralizing to the playerbase, as a whole. The social impact of a Ninja redesign must be considered. But not only on a Ninja class redesign, many other aspects of the game as well. None of this will make sense to some people at SE, whose only concern is their monetization method, which is flowingly, while players direct their discontent at the actual people working hard to salvage this mess, and Yoshi-P.

What players want is not more classes every expansion. The lack of a new healer class this expansion is not the deciding factor for so few people playing healers, the pointlessness of it is. SE tries to create an easy rotation playable for consoles and everyone, but does not stop to think to create a class meaningful to play for all kinds of dispositions of peoples and players. And even a singular, boring class can gain meaning in participating in varied content and situations where creative use of that class, even as a tool, is fun and rewarding.

Too many of the current concerns are dominated by "everyday breadwinner" type concerns. If Ninja topped BLM in even dps, players probably wouldn't even mind if the jutsus were twice as hard. But we know that statement is not true. It has to be reasonable. But SE weighs their classes around by "oh this class is ranged it should be penalized for that, melee should be rewarded", but doesn't stop to think "is designing raids to be ping-tests right"? Is tactical, not not even tactical, rotational perfection difficulty something meaningful for players? Should savage raiding following this philosophy and this form be the end-all of end-game content? Should we even want players having to do all this math, because we as engineers failed in our task, to balance content out, to do all the math here, so the players don't have to?

A failure in class design, a failure in class to make sense in a current patch, to make sense in the game (supportive melee??), is not just a failure in thinking up better rotations in-time for an expansion release. It always hints of deeper problems. Of wasted potential in some places, and misguided in others. Sometimes trying hard is not enough. The whole philosophy, process, workflow of class design might need to be reviewed. How you view your customers (just players to be put in their place, or ferried from one attraction to the next like a theme park ride?), how you expect your players would be happy from (you'd be surprised), and in the end, balance, theme, practicality, can these things save a game?

FFXIV has come a long way from 1.0, but is 2.0 really that superior? Even the ideal redesigned Ninja is just Ninja.
But the ideal Ninja may not have to be the player's ideal Ninja, as in, this does not define my childhood, but 'childhood' as whole. And this class does not define a class, but is embodying of the elements of RPG as a whole. In this case, also a MMO.
So think.