I know Thor and Hulk have female counterparts, but I'm here to cast people to be like the Thor and Hulk (and clearly the other avengers) we know from the movies.
Winona Ryder. She has shown plenty of depth in many different roles ranging from Girl, Interrupted, Black Swan, and Edward Scissorhands. She doesn't have much experience in comedy, but that doesn't mean she can't do it. RDJ wasn't as experienced, either, when he started.
Natalie Dormer can handle serious roles from her time in Game of Thrones and Mockingjay. She's a rising star and could definitely do well in some action sequences.
She also made out with the current Captain America. Does that translate into her own ability to portray him, probably not. Just thought I'd share.
Emilie de Ravin is Australian like Chis Hemsworth. You may know her as Claire Littleton from Lost or Belle from Once Upon a Time. She has very little experience in her own action sequences, but so did Hemsworth.
Kate Beckinsale known for her roles in Underworld, Van Helsing, and The Aviator. She has plenty of work in action films and could easily handle the task of a female Bruce Banner.
Gemma Arterton. Has been in a plethora of action movies: Prince of Persia: Sands of Time, Clash of the Titans, and Runner Runner. She was also in a movie with our current Hawkeye: Hansel and Gretel.
Domhnall Gleeson better known as Bill Weasley from the Harry Potter series. He can also be seen in Unbroken, About Time, and in December, Star Wars Episode 7.
Viola Davis has been in The Help, How to Get Away With Murder, Ender's Game and will appear in Suicide Squad next summer as Amanda Waller. If those stats aren't enough of an indication of how awesome she is and the characters she can portray, I don't know what is. She's definitely got that intense leader capability in acting.
So that's my cast for a gender-bent Avengers movie.