Hmm, I think you are wrong about pen and paper though, the social aspect and the possibility aspect of this gamingstyle will always beat the computerised verison IMHO at least.
To the question though..
I think that the click and search thing is one of the worst thing for any RPG games, you feel the "euphoria" of improving yourself all the time and that becomes the goal of any game. Thus the RPG facto will always be "tuned down" because of this. The best RPG game would probably be that of a text only interface more or less..
Otherwise we will always fight to be better, find the better armour, find a better sword and so on..
I think that the character develoment have to be more focused on skills and traits, feats and "more character powers and disadvantages" instead of magic items will lead to a better character developement. Online RPGīs could win alot by improving the interaction between players, chats and open dialouges, the possibility that you more or less have two teams playig bad vs good so you can have more intriguing adventures, a DM to the game can aslo change alot of the game to a more roleplaying style.
On the other hand, I work alot with puters and for me the social and fun connevted to pen and paper feels important to me, and thus I like the hack fest and the dungeon room by room action as a pure relaxation from normal behaviour
But most combat systems are already developed fine and I agree that the plots can be better, take PLanescape tormnet, to be able to play in that realm with thoose possibilities and thoose plots. Yes please!
Better plots are more important than more comabt features, at least in todays style of games!