Given how badly Daniel had wanted to come back to Atlantis, one would think that he would've done so as soon as the Ori Crusade came to an end. Instead, it took nearly a year and a half after The Ark of Truth. In-universe, though, it can be justified. The Milky Way would've spent the last year and a half recovering from the Ori Crusade (with the added issue of the hunt for Ba'al to make sure there wasn't at least one more clone still out there, as indeed Continuum proved). And since Daniel helped accidentally unleash the Ori crisis, his guilt complex would compel him to focus on that before his own needs and wants first.
:Likewise, Daniel may have also been overruled by Landry and the IOA on coming back to Atlantis due to how unstable the Pegasus situation became after The Ark of Truth (the Asurans, Weir's presumed death, Michael's Hoffan plague). Daniel may have had to wait for things to calm down before the SGC signed off on his return.
