This does seem to be a somewhat odd move - to a certain extent the comics and the movies now feed back into one another, which means that Marvel should really be seeking to keep the character identities in sync - Captain America should be Steve Rodgers (and should look pretty much like Chris Evans), it needs to be Tony Stark in the Iron Man suit, and so on.
Unless...
We do know that Chris Evans is under contract for 'only' three more movies (Cap 3 and Avengers 2 and 3). And, unlike in the comic universe, he's not immortal and unaging. So, if Marvel want to continue their movie universe indefinitely and avoid reboots, they'll need some sort of succession plan - either new actors take over as Steve Rodgers, Tony Stark, et al or (perhaps better) they retire the original superhero and bring in a successor.
So perhaps this is them starting down that road - use the comics as a test-bed for a new Cap (and Thor), and if it gains traction then they can make the same change in the movie universe. And if it doesn't work out, they can do something else instead.