The three player team isn't ideal, but it really made very little difference in the way the (present game) played out. If you as an individual (and a team) do not make alliances outside of your team, you are cooked. Before starting another of these games, I'd strongly recommend collecting a lot of feedback from lessons learned form passed team games.
There are many more distructive problems to this concept than the perceived advantage of a three nations team. I am playing as a member of the three nation team Frankly I have found my teammates to be more annoying than my enemies and I'm not allowed to attack them to correct their behavior. If anything being saddled with a second mandatory ally is a curse not a blessing.
Boosting the teams to 5 players might work, but as we have discovered int hese games the game dynmaic breaks down if the teams are clustered. Cypeg said it best, when he said that you simple recreate the Colonial (map) CF. Now I like Colonia, and the team game has some fun elements to it, but it's also very cumbersome and needs some tweaking.
The player that initiated this idea has since NMR'd, CD'd, and and abandoned all of his games at VDiplomacy. So it may be difficultt o recapture all of the ground rules for the concept. However, that's not necessarily a bad thing, since his rules were confusing, contradictory, redundant, and unnecessary.
In general when playing team games it makes sense to allow players to assemble their own teams. Equal sized teams makes sense too, but having a few singles or triples in the two man tteam doesn't necessarily ruin it. But for the sake of discussion, why not look at seven five man teams? Players could assemble their own teams or be placed into a pool of mercenaries that would be formed into teams of leftovers. However, to offer the game a truly interesting wrinkle, make the nation assignments random. That way there are five nations scattered around the map that must figure out how to work to their team's best interest.
Another angle would be to allow teams to form but NOT announce their membership until the end of the game. That way you would not be able to tell a mandatory team alliance from a forged alliance.