It was only in Paladin's Quest and Skies of Arcadia that this bothered me, but whatever. In Paladin's Quest, the color scheme for the graphics was such that it really hurt my eyes after playing for mere minutes. In Skies of Arcadia, the strobe effects for the special attacks made my eyes go funny and made me feel slightly dizzy. Granted, yes, in SoA you could skip the animation by pressing start, but sometimes I didn't press it quickly enough. Not convenient.
I don't like it when video games cause me physical discomfort.
Another thing I didn't like in Skies of Arcadia was that the camera was very herky-jerky during battles and made me feel seasick. In contrast, games like Grandia 2 had very smooth panning cameras during battle and I had no issues playing that game.
FF7 was a notorious culprit in this one particular niggle, and Nocturne did this in a couple of places too. I didn't like those segments where the camera was panned so far away from the prerendered backdrop that the player character icon was tiny, like the size of an ant. Were it not for the pointer thingie and the exit markers, FF7 would have been an exercise in navigatory frustration.
Various other issues mentioned, I can probably deal with, but the eyestrain and dizziness issues in Paladin's Quest and Skies of Arcadia are ones that are complete showstoppers for me, as well as herky jerky camera work; smooth panning please.