My biggest issue with the two team missions is that you never get quite what you were looking for in the other team. I hate how you are paired with another team COMPLETELY RANDOMLY.
If I could make one small change, it would be pairing teams up with other teams of similar composition; in the extremes, that means one player and seven henchies gets paired with another player who brough seven henchies. Likewise, if a team worked hard and waited in town for 15 mins to get an all player party, they at least deserve to have another all player party on their side. The in-between teams (with just henchie healers or whatever) can be matched with other in-between teams and it'd still feel fair.
It can be extremely frustrating to play on the missions where there's two teams of players. You go through all the trouble of putting together a party, meeting up, and starting the mission, and then... you get matched with one guy and henchies, and he can't keep Togo alive long enough for your party to get there and bail him out (that's even with a warrior running straight there). Repeat for three hours until you get matched with a team that doesn't die immediately.
Likewise, when I attempted the mission with henchies, I always felt bad when I'd get paired with a serious team that knew what it was doing, because my henchies sucked. I hated making them lose just because I didn't want to take the time that they had taken; on the other hand, I didn't mind being paired with more henchies then.
Two Team Missions are extremely frustrating
Miss Innocent