You should try to make sure that no character has an ability that's simply a weaker / more limited version of an existing ability in the old or the new set (I presume mixing will happen). A good example is ECO officer: you don't want a character that has a specific ability that you could simply do with the old Helo.
I guess that's self-evident, though. It's another thing if you decide an ablity in the old set is OP and should not be counted.
The admiral lost a bit with the inability to pick destination cards. Maybe tweaking the execution rule for him is an answer: perhaps it's not OPG but is still a skill check on a 10? Anyway, should probably be something usable with or without Pegasus' Airlock in play.