As a kid I played lots of Magic: TG, and what I now look back at as the funniest was playing not only 1v1, but 3 or 4 FFA mode. FFA basically means that there are no teams, and everybody is each others enemy.
Even though there will be some cards that are unbalanced in these kind of games, it is still worth it. Having an extra player or two to compete with adds a whole new dimension of tactics, and a hell lot of fun.
In the start, you should probably make this for fun, and not make you loose gold or score when you loose. This is becaue it would be easy dual-accounting and just pwn the player you play against. (2v1, you do the math. Even if one of the decks are newbish ones, they can dish out some damage).
You could of course add a lot of fancy stuff, like team playing and other things, but I rather believe that it would be better starting off simple and then expand on the idea if it works out.
Cheers!
PS: I'm failing at making a poll. Can't find the button.