User blog comment:Suparockr/List of Plotholes throughout the series/@comment-4950455-20120729072851/@comment-4953843-20120729084354

can't really expect them to stick to inconvenient color schemes now, can we.

blue being a more recognizable (and designated) hero color than red.

just one of those dev decisions for expedience.

(probably also had something to do with the first game being predominantly bluish with you as protagonist starting out your story as an alliance grunt)