Actaully, I kinda like the 4-button metal control idea, with a toggle to switch metal groups. BUT I don't think there's a good reason to allow anyone to be mistborn. I think that setting the game in the Mistborn 2.0 world would work better for those who like parties. Personally, I hate parties, but some games manage to be enjoyable despite them. With a party of allomancers, you can access multiple metals without the problem of having those overpowered mistborn dudes running around.
As an RPG, MMO or otherwise, hemalurgy or Lerasium could be used at level up to grant new metal usages and attributes. For example, if you start as a normal person, once you have enough X (money, xp, alignment points, quests, etc), you can get 1) a bead of Lerasium that adds the ability to burn a single metal or increases your power with a metal, 2) a hemalurgic spike to grant physical, mental, temporal, or sensory prowess (as the super-Inquisitors had), or 3) a hemalurgic spike to grant additional feruchemical or allomantic abilities. Then again, these could be handled outside the leveling system as permanent (lerasium, unremovable spikes) and temporary (non-harmful hemalurgic spikes) bonuses via an inventory screen.
The biggest disadvantage I see to this is that hemalurgy requires killing people. Killing people to level up, while an accepted method in video games, would make the character evil, period. And I really hate it when I can't play neutral.
What was that game that showed character hands and feet from first person and the acrobatic female main character? Is would remember, but I never played it.
I haven't gotten around to Mass Effect or Bioshock yet either, but they're just after the Knights of the Old Republic games on my list, and I just got them. Yeah, I'm a little behind the times.
Anyway, as Brandon has said, it's not the abilities of a magic system that make it exciting, but the limitations and what clever things the character can do with them. A mistborn who breaks into an impregnable allomancer-guarded fortress? Totally normal. Someone who can do it with nothing but nicrosil? Bad. Ass.