But to squeeze it out and make Pym a secondary, when its his discovery changes the mythos too much than they've done in the past.

No it doesn't. No more than leaving them out of the Avengers' creation entirely. (Apparently Tony now names the Avengers; Jan did it before.) And if the change means bringing a female character more into the spotlight, I think it's a great idea. The Avengers lineup is what, six white guys, two white women, and a black guy? Five white guys and one white woman if you focus on the core team. I don't think the team desperately needs another white dude. I'd say they have that niche well-occupied.

ANy way that I look at it, there just wasn't enough time of space to fit her into this, not without planning it out much farther in advance.

Uh I just explained two ways it could be done. You agreed she could have been the scientist character. And this: "but she can't just be made into a great spec ops agent. We already have Natasha for that, and to have two of them would be redundant." How does that not apply to Hawkeye? Why would Spec Ops Jan be redundant, but Spec Ops Hawkeye magically isn't?