Wow, a lot of stuff.
HR, that breakdown is real good; that Lost in Time trip sounds a lot like The Once and Future Thing from JLU, which is cool. I also like the Nomad episode, and heres why: Most of the best stories with Cap, Thor, and Iron Man play out in their own solo books, while dramas with Hank/Jan and Vision/Scarlet Witch usually play out in Avengers itself. But since an animated series wouldnt have the luxury of concurrent solo series, we ought to remember to include those iconic stories of the Big Three on this show as well. Im having to make a conscious effort to do that.
I wouldn't want to do a time travel episode right away, but I would like to do a flashback episode which shows Cap and the Invaders in the war, and that would parallel a case the Avengers are working in the present. It could be like "City of Stone" from Gargoyles. For the Invaders, I'd go with Cap, Bucky, Namor, Human Torch, Union Jack, Spitfire, Whizzer (possibly re-named the Blur, because...you know), and MAYBE Miss America, since her and Whizzer are a couple.
Interesting choice making Ms. Marvel a founder. I was going to save her for Season 2. And actually, Im starting to come up with ideas for Black Widow myself...