The first time around I beat the war with NCR. The second time around I won with Yes Man. Third time around I beat it with the Legion. Right now I'm working on Mr. House.

Is there anyone else you can win the war with?

So far my favorite playthrough is probably the Legion just because I like having atleast one Army on my side and my favorite mission is "Arizona Killer," assassinating the President of NCR.

No, but you can make the Independent army vary a bit

Whatcha mean? (By the way, Yes Man = Independent right?)

No, but your actions preluding Hoover Dam will have an immense impact on the Mojave for decades to come. One NCR ending, for example, could be drastically different to another NCR ending.

(Sorry) I'm a little lost. I've only played one play through with each Faction so far (Besides Mr. House) but it didn't seem like I had many decisions to make for the outcome.

The only thing I can think of right now to change it is letting the President die (or survive if Legion).