Well, a few things:
Unnecessary loading times. Now, I can live with loading if it only happens when necessary. I mostly don't mind with it taking some time for each area in FF XII to load, because I'll usually spend some time in said area anyway. And once it's loaded, it's pretty damn big most of the time. But when opening a menu or submenu creates its own loading time, then I'm starting to get annoyed.
Combat Adventure Games - my term for console "RPGs" like Final Fantasy - is a genre I like, but unless your battle system is really revolutionary, I do like a break from time to time. Even a silly little thing as the one-on-one battles in Suikoden V is welcome, especially since the execution there is done well enough to make it fun even when it's so easy (plus, it's not overdone either). But if all you've got is random battles, boss battles and plot, it does get tiring in the long run. So, put in some variety, a few minigames here and there. They don't have to be great, but at least make them controllable. Using casino games is just lazy and uninspired.
Having to go in and out of a menu to make a simple change, especially if you need to repeat it often. Iron boots in Ocarina of Time's water temple, anyone? Or how about changing front characters in Dragon Quest VIII (which doubled up with unnecessary loading times)?
This is a small point, but after Ocarina of Time and especially Mahjora's Mask, I thought it would be standard by now for most kinds of third person games to have more than two walking speeds. You know, to actually make proper use of that analog stick? Mind you, in the case of the Dual Shock, I'm not putting all the blame on the game developers, since that's the worst analog stick I've ever encountered. It could never handle the skillful archery needed in the Octorok-shooting minigame in Mahjora's Mask, that's for sure.
Heck, I mostly dislike the Dual Shock in general. It's designed to be looked at, not to be held. Wrong placement of left analog stick just to make it look more symmetric, for example. Not to mention that they are also just bad in themselves, having a convex shape and slippery surface (why didn't anyone tell them this is a bad combination? Why, why, why????) . And then the L2 and R2 buttons are uncomfortable to use. Heck, my middle fingers are never in a comfortable position whether I'm using them or the index fingers on said buttons, because it's simply not good to hold, no matter what. I despice it with all my gaming heart.