They didn't need to mention Morrigan in the sequel. They didn't even need to mention Flemeth in the sequel - that they did serves to keep her in memory, but also to account for one of the choices the player can make in DAO. Flemeth's cameo in DA2 is to keep her present in the world.
The thing that a lot of people don't seem to get is that, really, the Dragon Age games aren't about any particular player character or setting at all. DA2 caught a lot of flack because it wasn't epic, sure - not that it needed to be - but also because it wasn't about the Warden or about Ferelden, even after Gaider and Laidlaw stated time and time again that the point of the Dragon Age series was not about the Grey Wardens or that one little country.
The "main character" of the Dragon Age games is the entirety of Thedas, and the "main setting" of the Dragon Age games is the entire 100 year period. Each game has its cast of characters and primary protagonist and setting, yes, but the repercussions are not necessarily limited to those.
I see no reason to believe the team of writers would say "oh lulz, we totally can't figure out how to put Morrigan back in, I mean, there's only a few variables, this is too tough!"