How much technology did earth get from Atlantis before the city officially broke off? Conceivably, Earth could now be a technological superpower eclipsing anything the Goa'uld ever accomplished. They might even be able to make new stargates and ZPM's. They probably could overpower anyone else in the galaxy, depending on how much they shared with others; although the Aschen supposedly were able to defeat the Goa'uld, so they might be worthy foe. Are you sure Abydos wasn't completely destroyed? My impression was that Anubis' weapon shattered the whole planet, not just devastated the immediate vicinity of the pyramid.
There needs to be more work on the other human peoples. Is Earth reaching out to the former slaves? Are the Langarans? Is there any friction between the Jaffa and freed humans?
What if the Tok'ra got ahold of Baal's cloning technology? I've thought it would be neat to have a Goa'uld society that genetically engineered brain-dead human hosts, so the body would have only one mind in it and the Tok'ra would be freed from any ethical dilemmas. There's still the problem of reproduction, but cloning might solve that as well, maybe. Are Baal's clones only human clones with Baal's vassals taking them as hosts, or are the Goa'ulds inside them also clones? If they are, then the same technology could be used to maintain the Tok'ra population. Depending on just how advanced their knowledge, they might even be able to engineer a few clones into queens, or even engineer them into more human-like reproduction patterns, i.e., each individual can either bear or beget offspring, or maybe even both. This society should be blossoming into another technological superpower, although their numbers and the prejudice they face would probably limit their effective power. I wouldn't be surprised if the Jaffa start a war with the Tok'ra to permanently eradicate the Goa'uld species from existence, unless other human states started a war with the Jaffa, since they likely wouldn't care much that the Jaffa were technically slaves when they were committing all sorts of atrocities against humans. There could be a sort of Galactic Cold War going on, with Earth caught between the Jaffa, Tok'ra, and human states, trying to remain neutral with it's friendly ties to all groups.
The Wraith need to be gone. It will need some deus-ex-machina. If the Ancients could not defeat them, then there's no way the earthlings could. Perhaps the Wraith and Orii could defeat each other. The Orii learn of the Pegasus galaxy, decide that converting the primitive humans there would be easier than dealing with the Milky Way, start a war with the Wraith, and get curb-stomped. Then the Wraith find a way to migrate en-masse to the Orii galaxy, which of course would remove them from the protection of the Ancients, allowing the Orii to deal with them directly. But after the failed invasion, they don't have the mortal resources to continue with their crusade, so they have to wait a few generations to try again.
Atlantis would be in a strange position. Are you sure it should be broken off from Earth so soon? If they have a decent population, they should be the only significant power in the galaxy. The Genii can't even match 21st century Earth technology, and have only been a real threat because of their numbers and their strategies. With a fully populated Atlantis, no native civilization could even begin to compare. They will be able to unilaterally dictate the development of the Pegasus galaxy, should they choose to do so.
These are just a few quick thoughts off the top of my head. I'll be interested to see how it turns out.