My guess for the alien invasion is that it will either be a dream sequence or only a few come to earth and get mistaken for IF's. I could see the aliens taking advantage of Frankie's caring nature somehow... or just driving her nuts.
I'd like to see more of Frankie in the new episodes but I'm kind of drawing a blank at the moment as to how.
I think what I would really like to see is Frankie have a girls-night-out with Kathy (who would always be conveniently off screen or hidden behind something and never heard because Bloo would always cut her off.) only to have Bloo tag along.