When we turn on our machines made by Sony, Nintendo, Microsoft (if you're unlucky), Sega, or whoever and put in a new RPG, we have a pretty good idea about the character we're going to be controlling once the opening scenes, history lessons, and ear-agonizing beginning music videos are done with. We safely assume that the androgynous little freak in the bad clothes who walks around in circles to our grubby fingers' commands is going to be the main hero of whatever epic conflict and quest he finds himself in the middle of. This isn't ALWAYS the case, though.
For example, in Final Fantasy Tactics Advance, the protagonist of the game, Marche, is NOT the main hero. The game doesn't seem to really have one; Llednar is probably the closest to being one. Marche is actually the main VILLAIN. He's a classic FF bad guy--his goal is to destroy the world for strange, outlandish reasons that just about no one else in the world agrees with. The only real difference is that, for the first time in SquareEnix history, Marche's outlandish reasons for world-conquering are actually GOOD ones, not just stupid and misguided like most villains with a "lofty" goal to their actions ("THE WORLD IS SO DARK AND PAINFUL SO I'M GONNA KILL EVERYONE TO SAVE THEM FROM IT BECAUSE KIDS TEASED ME AT SCHOOL LOL"). The point, though, is that, even if he does the best thing for the best of intentions as a very decent and well-developed person, Marche is nonetheless the game's villain rather than hero.
That's a rare quality for an RPG main character, to be sure (Knights of the Old Republic games don't count, either, because you have the opportunity to CHOOSE whether you're hero or villain). And it's done VERY well, exploring Marche's perseverence for his ideals yet doubts about his right to do so in such a quiet and complete manner that most people won't even realize he's taking the position of main villain instead of hero until you mention the idea to them.
Another interesting oddity in protagonism (is that a word? I'm claiming it as my own if it isn't already) can be found in Dragon Quest 5. Now, my opinion on the Dragon Quest games is pretty much the same opinion that I hold on bacterial infections. However, that doesn't mean the games don't have a few good qualities hidden beneath the bad.
Now, in Dragon Quest 5, your nameless, personality-less protagonist is, indeed, a good guy. He has some adventures as a kid, gets captured for slavery, escapes as an adult, has some more adventures, gets married, has kids, gets turned to stone for like 15 years, and then gets saved by his kids. But as heroic as this guy's actions, if not any words from him, indicate that he is, it's his SON, not him, who is the legendary main hero person who wields the legendary main hero person's sword against the demon king bothering everyone. From a perspective, the game's protagonist is just the random father of the game's main hero. Most of the plot could just be seen as a long backstory for the true (somewhat short) quest of the son.
The idea's not taken very far or developed (nothing ever is in that series), but it's still there, and still a neat concept with interesting potential that your character's role in a game could be no more than an accomplice of some sort to the game's main hero.
Another uncommon trait in RPGs is the choice of selecting who YOU want to be the protagonist. Games like Star Ocean 2, Live A Live, and Seiken Densetsu 3 give you the option of who you want to be the protagonist and main hero of the game, which is neat. Though it's rare that any major changes to the plot occur depending on who you choose, it's still a nifty idea to be able to choose who you think is the real hero material of a game. In the same vein, an RPG which has more than one protagonist is also an original idea, such as Final Fantasy 6. I've never been able to see anyone successfully prove that Terra and Celes didn't share the roll in that game.
There's really a lot game developers can do with their games just by switching the role their protagonist plays. Sure, it's fine to play through a game as the main character, and there's still plenty of potential for interesting and gripping ways to develop a protagonist as a main hero (Virginia from Wild Arms 3 is a primary and reasonably recent example of this), but there's a virtually untapped wealth of creative freedom to build a unique tale out of a protagonist who's not a main hero, or not the only one, for whatever reason. Game companies really oughta try it more often, because you can get really great results with a little creativity.