Combat and exploration that suck.
No RPG in the last decade has nailed both of them, and few have come close. I've watched so many promising real-time and turn-based games turn out bland, sluggish, unpolished, complicated, absurdly stacked towards the enemy, or some combination thereof. I believe I've found the root of that problem.
Half of these RPGs aren't designed for the computer, the console, or any other electronic device. They're designed for the tabletop, by tabletop people who know or care more about fantasy worlds and fantasy stories than about computer games or even games in general; CD Projekt, Troika, SSI, and early Square-Enix come readily to mind.
The other half are from the sim types like Piranha Bytes and post-Daggerfall Bethesda, who are so lost in delivering a realistic fantasy life experience that they'll let the framerate drop to 10fps on decent hardware and modest graphic settings (Gothic 3) or think I'm supposed to enjoy robotic combat with lame stock sounds in between holding W+Shift through a featureless world of gold and brown and gray (Morrowind).
Sega didn't fall into this trap so easily with Phantasy Star 1&4, because they were mainly arcade people. Dynamix scored a hit with Betrayal at Krondor, as did Spiderweb with Exile and Black Isle with Fallout, because they were actual computer game people. Their knowledge, experience, and care about the human-to-computer interface lent their games a certain touch, without which many competing RPGs and equally complex games suffer greatly.
Though a full course on the subject is beyond me or this post, it really helps when the game is smooth and reasonably paced and actions feel as natural to you as to the characters.