What you're describing is just the current materia system expanded - and the reason the current system is limited and restricted you've already stated, thus kind of making this thread sadly redundant. Yes it would be great to have bonuses to personalize your equipment with, but you said so yourself, SE are trying to avoid situations where players are discriminated against for "not having a certain equipment setup" like what FFXI suffered from. Sadly I don't see SE changing this any time soon.