Seems pretty damn reasonable. If the game really spends most of its plot screaming "THE REAPERS ARE HERE, THE GALAXY IS DOOMED," and emphasizing the need for galactic readiness and Taking Back Earth and whatnot, and then Shepard is off picking up space kittens then it'd be a little weird.
You could say the exact same thing about ME1 and ME2. Hell, just about any RPG really. None of the side quest in the previous game has anything to do with the collector threat or saren/sovereign.