Ben with a team would have been very interesting. I would have had Ben with Rook for a season, then in Season 2, Ben and Rook would be "leaders" of their own teams (made up with the Plumbers Kids, and other people with powers they'd introduce and then have join the team)
I'd have liked to see them explore more off world, as those episodes tended to be fun, but it was difficult because there was always some threat on Earth at the same time.
Seeing progress with Ben actually locking up villains would have been appreciated too, since it seemed like most criminals were right back on the street a few eps later. (and with all the security features the Plumbers had, I can't see someone like Liam just breaking out every single time...if he even could. So did they not arrest him or what?)
I think it'd have been good to explore using combinations of alien's powers. Obviously, Ben couldn't switch between them all the time, but having him be Stinkfly, shooting goop on someone, then switching to Heatblast and blowing them up would have been awesome.