A combination of minor modifications on certain pieces of weapons and armor, and a customization system utilizing skill-enhancing materia would be a fine idea.
Yoshida said he feared that skill enhancements on equipment would take away player choices in gearing.
Yoshi P, I love you forever, but sir, what choices?
i70: Crafted, Darklight, Darklight Equivalent in Expert
i80: CT gear
i90: Myth, Allagan, Crafted
i100: Weathered Soldiery
i110: Soldiery +1, High Allagan
That is it.
We are not awash in choices, and we are not awash in gear, either. A group farming up to turn 08 will generate six 110s a week among eight players, plus the Oils. Can farm one accessory from Soldiery a week, or most of (but not all of) an i100 primary armor a week.
We do not have a five-star restaurant menu of choices going for us here. Dev Team fears boxing themselves in, but they need to remember two big things:
#1: They are bound only by imagination. This game is their oyster. They can take any crazy number of ideas from these forums, BG, or hell, reddit, or dream up their own. They need not make the modifications excessive or game-breaking, merely interesting. Situational. Remember when stuff was situational? I do. I loved that. o.0
#2: Taking the OP's first concern up, so what if a particular piece of, say, 150 gear is slightly outstripped by a 140 with Brutal Swing: Stun Duration +1s in someone's view? If it is worth it to them, let 'em do what they want. People do this already, utilizing i90 crafted gear to load up on secondaries and using that gear in Coils instead of certain 100s, or even some 110s (though in my opinion, ya gotta be crazy to skip a 110 for crafted breadth of secondaries.) Player choice is not a bad thing, and Spineshatter Dive: potency+50 is not going to annihilate all balance in the game. We already have folks sequence-breaking Coils simply by piling on the damage faster than Dev Team imagined they would, or solo healing turn 9. C'mon.