I was wondering can you get all achievements at the end of the game, but i know that isn't possible because of good/bad karma but generally can you get all achievements after you beat the game. So could i go all the way to the final mission and then get most of the achievements and then start over and get the rest.

in 2 playthroughs, you mean? I dont think so. there are 4 different factions to side with, and I'm pretty sure each one has a achievement/trophy for completing the main quest. you could save time by being somewhat neutral throughout your next game, and when your about to choose a side, just make a save you can go back to and pick another faction.

This is a game that you can't complete in one or two playthroughs. Which is good, I ignored a bunch of quests on the first play through, then did some of them on the next, etc.

I think one could do it in 2 to 4 playthroughs, but you would have to play the game in such a way as to know the complete story so that you do all the intermingled quests the right way. While that is a way to play, I would rather enjoy the game as it is revealed to me the first few times through. Then go back and see how much I can get done in one or two play throughs, or complete obscure side and free quests. But that's just me.