Okay, here's a really weird technical tip but I swear it works and has been confirmed many places elsewhere:
While loading after a mission, if it's taking a long time to load you can just hit the CAPSLOCK key. The game will stutter for a second, then it'll load immediately.
I know it sounds like one of those crazy sounding things that gamers do because of hearsay, but I just checked. This won't work if you have a slow HD and if your system is slow in general due to hardware, but if you have a powerful PC and it weirdly takes forever to load back into the Avenger after a mission, this will help. I haven't tried it during pre-mission loads though.
On the other hand, after trying it a few times more just now, it might have caused my game to crash. So yeah, this game has a lot of weird technical issues.