Ability/passive equip systems are a good idea as well. Having 4 bars full of abilities is distracting and counter productive to creating a functional strategy without using many addons or macros. (I realize you didn't mention active spells - but I wanted to add that in there since I felt they are easy to talk about at once)
I would be interested to hearing such a system - GW1/2, Diablo 3, are obvious examples of this system (for active abilities).
While D3 failed to make as many builds as it wanted*to make, it -did- make a couple builds quite viable even end game. Which is exciting - as it is now the only builds you get to do in FFXIV are item builds.
* D3 has had a recent patch to buff unused skills to make even more viable builds - haven't checked it out if it is true, but its good news for those who are still playing.
Obviously passives would be easier for the dev team to come up with - and still maintain a fairly FF feel. And if they did active selections like the above games did then they would have to greatly increase spell count for each class - which would probably feel less FF unless you were a blue mage.
(Passives are a lot like perks however, just able to switch them in and out easily unlike say WoW - though you may in D3)