While we don't know the specifics of what Marvel didn't like about Wright's script, don't you think if they objected to something like who the male and female leads of the story were, that would have come up sooner? I mean, if that's a problem, then that's the very first note. They're not going to move the film into production and start casting if they disagreed on who the lead characters were supposed to be.
The movie was always billed with Lang as the hero and Pym as the older mentor who passes the torch, from the very beginning. That's the concept Marvel got behind and stuck behind for all those years.
You forget that Wright had the scripted storyline before Ironman 1, and Ant-Man was originally supposed to be a Phase 1 movie.
Joss wanting to use Wasp was likely killed because Wright delayed Ant-Man to a Phase 2 movie.
It is very probably that at this point in time, whatever Wright was planning on doing with the movie originally needed tweaks to line up with everything that has happened in Phase 1. Wright delayed the movie again, so now it's a Phase 3 movie.....
Captain America 2 happened. Everything changed.
Avengers 2 has been written around Ant-Man not having happened yet....
Marvel tried to do it the Wright way, but it took too long and all turned out so, so Wrong.
So I don't think it's an issue of who the main characters are, it's more that they should have been introduced years ago, and now things had to evolve to not include them.
At this point, the MCU has grown so big, that the mostly stand-alone story needed major revamping to tie it into everything else. I'm sure that's where too many changes were being made, and Wright could no longer call it his movie.
I wouldn't be surprised if Marvel's patience just ran out and basically told him to either get with it or walk, because they were not delaying again, and already altered too many pre-planned story points waiting on him to make it happen.