User blog comment:Ygrain/ME sequel: what shall we do with the extinct races?/@comment-2250460-20121123171304

You missed one race, the virtual aliens who are killed in Destroy.

Anyways, here's how I figure it:

Krogan:Some lame excuse were they were cured of the genophage by someone else besides Shepard.

Quarians:Some lame excuse were it is revealed that the geth did not kill all of them in the Space Battle above Rannoch, rather they destroyed the military ships.

Geth:Some lame excuse were they are rebuilt by the quarians.

Unfortunately, all these explanations are rather lame and or just simply suck. Easiest way to do it is just to make these three races not plot important, so if they are extinct, big deal.