My favorite by far is V1. And I agree #1-28 is by far the best of the best. Some of the later stories in that run were good also, but the early stuff and team will always be the best in my mind. V2 I enjoyed. It would've been nice to incorporate more of the originals. Might have saved the book. V3 I didn't care for, other than the fantastic artwork. Clayton is my favorite Alpha artist now!
My dream team would be(using members of all teams):
Heather and Mac - working as government liasons and heading the project.
Shaman - in a medical/mentor role. Whitman Knapp as his assitant.
Field Team
Guardian - Radius assumes the mantle after he is recovered by the Mole Man's moloids. Being buried alive can change a man, can't it.
Sasquatch - the only real answer for muscle.
Puck - I'd have said Zusha if I meant her. Eugene covers the espionage angle well.
Talisman/Shaman - Elizabeth assuming the role we all know she should.
Flex - more confident and in control of his powers - perhaps expand them to allow computer systems interface.
Jefferies/Box - It'd be interesting to see him interface with Flex if the computer interface thing evolved - He also supplies more muscle.
Last but not least....
Zusha - she's gotta get her own moniker though. Puck is taken!
I'd keep characters like Pathway, Snowbird, Wild Child, and Diamond Lil around for special assignments.