What my team does is play an I formaion. We send one front player all out to control the flag (not necessarily pull it, but deny the other team the points from the pull). The second player plays a mid position, and the third plays back. The 2nd and 3rd both sweetspot on opposite sides off the break, while still remaining behind the starting bunker, this allows two oppurtunities for a quick sweet spot, which is essential to dominating a 3 man. By this time, the first has reached the center bunker or another capable position, at which point the 1st and 3rd players lay cover paint while the 2nd player rushes forward a bunker. Thus, we are set up in a "power I" formation that can easily dominate 2/3ds of the field. With the small size of a 3 man field, we dont really have to worry about a flanking move, and any fool that tries to bunker our 1st player will either be picked off before or during his/her move. However, this can turn on us, if any of our players are eliminated, and we are forced to play man down, then we try to consolidate into a corner and just try to outplay the other team and try to make something happen.
I agree that the key to winning a 3 man is to simply be better paintballers. Grand strategies and excellent teamwork on such a small level are often beaten by finely timed moves or excellent shots, with such a small number to work with, any game plan must be flexible, and the players have to be willing to occasionally scrap the plan and simply play their game.