To make an alliance game feel like an alliance, I think that as long as 1 or all team memebers are in an area, both of them should get points for holding the area, but divided among them. Example: 2 player team in one territory that gives 2 points, 1 to each. For 3 player team, the lowest area is 3 points. Even points on territory for 2 players and odds for 3.
Even though they are only allies, they are playing as a team. This gives both teams the ability to conqour one or the other as a team. The trick is to have each player start in one area next to each and expand on neutural territories. Points added differently, say 2 for one or more area, until both or one member of team gets the whole territory. Also, you can fortify trough your ally. Another suggestion, team member chat box, so the other team doesn't know both of your next move.