Well, since I seem to be thinking about weapons, there's the matter of making every character only able to use one weapon. This is used in the later (PS) Final Fantasy Games, Chrono Trigger, and a gazillion other CRPGs. I don't see terribly much point to this other than laziness, especially for combat-centered characters. (Casters can be kind-of excused because presumably they've been spending time on learning spells rather than on weapons training.) At the very least, I would try to make some basic weapons that everybody can use in the beginning, and then some more character-specific weapons later.

I guess this is more a matter of personal taste than some other things are, but I liked being able to shuffle weapons between people in FF6.

It also seems silly to me how every newly-accessible town has more powerful weapons and equipment than the last, even if it's a tiny hamlet in the middle of nowhere. I would prefer being able to enchant/upgrade weapons and equipment, possibly through quests. Of course, this was rather annoying in FF8, but that was because of those bloody magazines you had to find before you could forge weapons.

If you hadn't noticed by now, I speak mostly from experience with console RPGs. I have tried several PC RPGs, and I keep getting lost and stuck...