Why not borrow the good parts from FFXI?

[KisaiTenshi]

Massive city battles with invading forces.

V1.0 had this, various other MMO's have this. It generally results in not being very fun for the people who don't want to participate. Like ideally, the mechanism for this is to have a city that is regularly assaulted by various classes of monsters (eg from easy zombies to hard dragons) and you have to participate in some meaningful manner to get any reward. It could even be done in a way that crafting and gathering classes can be used to build defenses.

However as much as I like the idea in concept, in practice, players and bots just zerg the map and no strategy is involved.

Ferry/Raft rides with random events.

V1.0 also had actual "ferry" zones. Well, until they got rid of the Ferry entirely. Another MMORPG I've played had something like this as well. To get to a "fishing ship" required triggering a certain event.

Meaningful exploration with difficult mobs, mazes, unique pathways, and things to discover.

What people want when they ask for "meaningful exploration" is that they want dungeon/tower/castle type locations that actually require "solving" (eg "The Sunken Temple of Qarn"'s type of puzzles but actually open different paths through the dungeons, and they change if you don't solve them correctly.)

Skill-based battles rather than combo-spam.

Combo-spam is what every turn-based system uses because that's what is less cheatable and most fair, it also gives it enough turn around time to verify that the combos and skills are valid. Action MMORPG's (where you have to manually dodge as well) are extremely cheatable and tend to suck if you don't live in the same city that the servers are in. This is why many Japanese and Korean games tend to suck when they are localized to for North America/Europe, because they don't have the sub-16ms (1 frame) latency to allow all players fair play.