Probably because it's presumably more interesting to be the underdog in the conflict, aka the guy who doesn't have all the bug guns on his side. Not to mention if you armed the player with all the best stuff right off, it wouldn't make for much of a challenge.
Of course, it also depends on the game in question. In NV, you can ally with either House or Yes-Man and the army of badass robots, foster good relations with the Brotherhood of Steel, end up effectively owning Big MT and kick the ass of the most technologically inferior faction in the game.
