It is worth noting that there is a difference in comparing jobs to each other and comparing jobs to themselves.

In the case of comparing jobs to each other, ie. party composition, you don't necessarily take the highest DPS jobs as different people prefer different jobs and as a result, they are more likely to play and get better at said job, meaning they will perform better than if they played as a "higher DPS" job.

On the other side, comparing a job to itself, you want to take the best version of that job you can. Why should someone use Spec A when Spec B is just better in every way. This then isn't a case for job preference, but your functionality in the team you are in. This is likely why people are more strict when it comes to balance for a job itself when comparing it to itself than comparing jobs to each other. I'm going to take a PLD, when is the best PLD I can take.

On that subject, you might think your ideas provide no DPS benefit, which they don't really, however, how many provide useful utility that is just a great help in general? Again, just looking at your ideas for PLD;

Cover with 20% mitigation, useful in SB, don't see why it cannot have it's uses here,
Hallowed Ground having a 5 minute cooldown, insanely powerful, more uses out of (almost) complete invulnerability is just going to help in many scenarios,
Cleanse on Intervention, ok, how often is that actually useful? I assume the comment on P12S's tank buster is in relation to this, but if the only thing is one specific mechanic, it doesn't seem that useful, especially if you consider a shorter Hallowed Ground to (I assume) just invuln through.

So, you have 2 useful ones and one, questionable. Already you can see where people will say you have to take either option 1 or 2. However, between these 2 options, which one is better? Maybe, it is fight dependant? Which leads to the next question, how easy is it to swap between different options? If it is simple, why bother with the whole 'materia' thing and not just have it as a menu option? If it is also fight dependant, people will expect you to have the right materia for it as well, strats for PF at least will be made with specific specs in mind to make the PF life easier, this then defeats the point of it being a personal choice as, again, we are back to it being required.

On the flipside, if it is harder to swap, people will complain, especially if you have to swap several times throughout the savage progression. It just turns into needless busywork.

What a lot of people forget, just because they only focus on it, is that DPS is not the only thing you have to consider when designing a fight, a tank's mitigation kit and a healer's healing kit also have to come into play. You can design a fight that requires specific setups in order to win, which leave no choice, or you look at the basic kits, design fights around that and leave it up to the player to choose what to use, at which point certain things can destroy the balance you have crafted when designing fights, taking away that initial challenge you set out.

This again comes down to, to try and make a choice, but in reality, there is only the right choice and the wrong choice and noone wants to pick the wrong choice.