If you mean Single Player, yes.
If you setup all 6 ships for 1 team in Base assult, and the computer will add some ships for another team to balance.
Also, in Wolf359 mission, computer will add 1 Galaxy, 1 Norway, 2 Saber for the anti-borg side. So at maximum you can have 11 ships including the Cube in this mission.
There're some custom scripts which can allow more than 6 ships in SP skirmish, e.g. Spawn, Fleet Pick, and Team TNG Battles.
wtf are you talking about? Ships or players? He asked about players. In an IP game there is a hardcode limit for 6. Same for the Dyna. But in dyna missions, unlike the limit of 3 ships in an IPgame, you can have 6 ships for every player. But only 3 can be outfitted in spacedock. To outfit them all, ED's DB editor needs to be used.
