I think you should go with a group of 4 so that there are two couples.

My reasons:

1) I don't want to see a love-triangle. Most of the time, when I see it I feel that it is artificially added to cover up a weak plot. But since your plot is about emotion, you could have a stronger reason to have a triangle.

2) One thing you didn't mention, but I think is important, is that your plot (as you posted in another thread) has this structure:

0.1 - A group of friends win, everyone is happy.
0.2 - Something happens to mess them up.
0.9 - They struggle and fixed everything
1.0 - Everyone is happy again.

Suppose you want to highlight the fact that everyone was happy in the beginning, then your thought to give balance was important. It will give the player a better emotional footing to identify that the group was happy in the beginning, but something screwed them up. I think that you initially chose a group of 3 because that is the mode. You don't have a reason to pick this number other than to mimic some other stories. But now there is a reason to have a group of 4 and your intuition is breaking out from your borrowed mode to tell you that your design should have 4 characters in the beginning.

I agree with Elhrrah that the design needs game play consideration. Although you could still decide whether the characters would always fight at the same time at the same place, or that they would fight individually, in pairs, or in a group of three (with one of them disabled). So you could really decide in either order.

Structure Example:

0.1 - Group was happy.
0.2 - Event occurs and member D is particularly unhappy or disabled
0.3 - Group is disbalanced, member C tries to get D back and/or while D wants C to break from group
0.9 - Group holds itself together and triumph over the disturbance.
1.0 - Group is happy.

Yeah after reading through the past comments and again having help from Wai, I have decided to add the fourth character. The story was originally going to have just 3 but as Wai said this was pretty much based off other games that are usually groups of three. I plan to have it that the player starts off with the four characters fighting together and for some reason, one member is taken from the group, leaving only 3. Then the players mission is to go and retrieve that character from somewhere and game play would continue as normal. I also have had another idea concerning the characters and the game play but I think i might keep that private for now, just in case.

Cheers,
-James-