A sort of Stargate Next Generation
that's what i'd really like to see out of the franchise, frankly. i had a discussion along very similar lines towards the end of season 4 of Atlantis. i have to agree with Annatar that Atlantis has suffered numerous problems.
i think the biggest one was simply timing. Atlantis was barely getting on its feet while SG1 was on its last legs. they even sort of admit in several places that the ta'ri re-made the galaxy, killed all the bad guys, and managed to do it all while keeping their planet's population blissfully unaware. as pointed out, not really anywhere else to go.
on the other hand, the SG mythos allows for intergalactic travel (and not just milky way to pegasus). i find it hard to believe they'd run out of potential bad guys in a strictly matter-of-fact way. but the thing is, SG1 operated on the same kind of good/evil plot tension as Star Wars. would you make a Star Wars movie after defeating the Emperor and restoring the Republic? (well, i think Lucas intended to, actually).
what i see happening in season 5 of Atlantis gives me a little hope for the series. with Weir and now Carter out, Woolzy's filling the role of comic relief and the show seems to be bearing down on Shepard, Tayla, McKay and Ronin as the main characters, closely corresponding to O'Neil, Jackson, Carter and T'ilk (the humorous and supernaturally lucky leader, the cultural expert, the technological expert, and the muscles that are fun to look at... okay, maybe that part's just me).
also in the most recent epi of atlantis, they travel to some random parallel universe and see an enemy they haven't seen in this one. i'm hoping that enemy becomes more regular, since they seemed both powerful and enigmatic (perhaps if for no other reason, they were only glimpsed breifly).
but... i dunno. i'm still hoping for a new Trek series.