No, it's not supposed to be like that. One of the issues right now is that a lot of people seem to be quitting after a game is put together (often at the load screen) because they only want to play with their friends on their team, and for whatever reason don't want to just play customs. We are planning to add team pantheon, but right now that seems to be the main issue throwing things off.
While I completely believe that this is one of the major reasons for the problem, that doesn't mean you get to just say "Well that's why it's happening, so oh well". The truth is, you made an exploitable system. Now Stardock needs to work towards patching the holes that allow this to work. Let's examine the issue more closely:
Question: Why is it that people are using this method to play with friends as opposed to Custom games?
Answer: Rankings. People are using it as a method to exploit the ranking system. In Custom games, almost everyone with extremely high rankings plays with friends, so the competition is difficult. In pantheon, you're almost guaranteed to win playing with friends since it's a supposedly "random" system. Also, a lot of people would say that a high ranking Custom Ranking doesn't "mean as much". Obviously this is silly, since these stats essentially mean nothing and they're going to be reset soon anyways, but this is the train of thought people take.
Question: Why won't simply implementing "Team Pantheon" fix this?
Answer: Once again, Rankings. Once you have a Team Pantheon system, you will only see arranged teams playing in this. Personally, I'm ecstatic to see the increased competition. I think it's going to be a ton more fun and present a great challenge. However, I have the feeling that the rankings junkies won't see it the same way. These types of players are always looking for a way to make the game easier for them, and I've seen it ever since I began gaming. Maphackers in Starcraft, Standby glitchers in Halo 2, and exploiters in World of Warcraft arenas are just a few examples. They don't care about improving their gameplay, and they don't care about playing fair. All they want is to have a good ranking so they can feel better about themselves. These players will likely keep playing the regular Pantheon games and include their friends so they can continue facing PUGs and boost their stats.
Question: So then, how do we solve this problem?
Answer: The answer is simple. The method of being used in order to make this work is to have both players enter a Pantheon game at the same time, wait until the connection information screen shows all the players attempting to connect, and immediately leave if they don't see their friends name on the screen. We solve this by not allowing players to see each other's names in the dialog screen. Put in some sort of placeholder until the game begins. (ie: "Player 1, Player 2, etc") This way, the player will be forced to enter the actual game, and at that point if they decide to leave it will cost them a loss on their beloved "stats".
Question: What if this isn't the only thing causing the uneven games?
Answer: One of the other major logical problems with the game is how Pantheon games are formed. Unlike a custom game, it is all automated. In a custom game, you wait for your desired number of players to join the game, allow everyone to connect, and then once everything is peachy you begin. However, in a Pantheon game the logic is very different. The Pantheon system finds the desired number of players, then quits looking for players completely and lets them all try to connect. If someone cannot connect, or leaves, then they aren't replaced. The game is simply started without that player. All that needs to happen is a change in the Pantheon logic. Find the necessary number of players, let them all try to connnect, then determine if anyone was lost in the process. If they are, find another player(s) to replace them and start the process over.
Question: Can I have a job Stardock? Please?