Actually, there are a number of things I would have liked to have seen with Atlantis.
Much like they did with McCay, Atlantis was the series that would have allowed the powers that be to have given favorite secondary characters more of a presence in the franchise. In fact, I would have split things up a bit at the SGC and might have gone a route similar to this.
1) Daniel as the head of the expedition. C'mon-- he's the foremost Ancient expert. As much as I like him on SG-1, Shanks would have been great on Atlantis and a very logical fit.
2) Jonas replaces Daniel at SGC. I'm one of the few folks that like Jonas Quinn but they could have brought Corrin Nemec back into the series with Mitchell, Carter, and Teal'c as the new SG-1.
3) Camulus (sp?). I always felt that his potential request for asylum was handled too quickly. Fine-- you want asylum, we'll give it to you. You're going to Atlantis to assist the expedition in getting the city up and running.
4) Ditch Teyla. Honestly, she's never really added much to the series IMHO. For some reason I've just never really grabbed onto the character the way that I have much of the cast (and supporting cast) of SG-1.
5) Lt. Hailey. She was touted as the "up and coming" Sam Carter so why not use the secondary character on the new series. It would have made for an interesting cross-over.