OK...

I just got about 2/3 of the way through the game an i realize i am helping the Legion out based on my actions..when i thought i was helping the NCR...!! WTF.

Ill explain... I thought by taking out House, that the NCR would be better off, in addition setting up the wildcard scenario to aid them. come to find out.. this wont exactly happen and i run the risk of the legion winning..

SO...

WHo is the good guy?..is it in fact house? with NCR as the annoying faction and legion evil? or is NCR the good guys and house the Evil one and legion the annoying faction?

There's no clear cut "good" faction or "evil" faction, that's part of the point

Yes the legion are the good guys, only they try to hide it by enslaving and [censored] people.

I had a similar problem, although not to such an extent. The game doesn't make it clear that eventually you will HAVE to side with ONE single faction, and eventually it forces you into an ultimatum that may not turn out the way you wanted it to.

The Boomers quest line locks you into a faction; IE whoever's help you enlist the boomers for means that is your endgame faction. So if you haven't got to the Boomers yet, you're still in the clear but if you have and you've enlisted them for someone other than the NCR, I'm afraid you're working with them endgame.

I actually cared about this 1st playthrough, and realized the game ends at hoover dam, so now i dont really care because your basically just deciding what slide show you see.

Not true i enlisted the boomers with the NCR and then went out and decided to take new vegas for myself.

I'm loyal to the NCR, due to the fact that they are similar to a pre-war nation, in the long run they might be the best bet on rebuilding humanity IMo