If you are doing a multiplayer game
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I think it's important to be able to make very individual characters with lots of different skills to choose from (many skills quarantee possibility to do many different things). Then ofcourse interaction possibilities with other players are also important.
And possibility to affect the world permanently, for example, if one could build a house at some point it would be awesome, but ofcourse it's pretty difficult to implement.
If you're doing a singe player game
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You might still consider the option of allowing multiple players. For example support 4 player multiplayer mode.
I think the story is pretty important in single player RPG. You should have the main plot that goes from the start to the end, and then fill the game with smaller plots that keep players busy. I just had an idea of having the main plot being pretty small (like finding the cure for player's soon to be wife's genital herpes.. just kidding and when player is reaching that goal, the smaller plots could actually be a lot more important, so that player could save the world (maybe couple of times) while he's trying to reach the main goal.. Just an idea though..
Then about rising levels. I don't think it's good to just add some hitpoints and hit probability when player reaches higher level. But if player would for example get more skills that he can creatively use to achieve different goals, it would be pretty cool..
And you should avoid linearity by all means necessary, I hate rpg games that are linear.. You might encounter something in game that you cannot handle right now, and you just have to give it up and come back later when you have tools/skills to solve the problem.
That's pretty much it.. I have a lot of ideas for RPG's since I'm planning to do one myself (one of these days), but I'm too lazy to write all of that down right now
Couple of more things tho (that I just thought of).. Don't make just combat spells, since combat is what fighters are for. Make spells creative and make them for very different purposes (ofcourse this adds complexity to creating the game, but..).
And learn from Half-Life! Use scripted encounters if possible. You could have goblin's escaping with wagons just after they have slaughtered and robbed some innocent (or maybe not so innocent.. make twists to the plot) travellers.. Or you could have a big monster that's way too hard for players to kill, and the solution for problem could be like shotting fireball to a big tree so that it falls on top of the monster, and kills it.. or something.. you get the idea.