@LokiDionysos: the idea of all the magic in the MCU actually being science, some of it not yet understood by people on Earth, captured my imagination when I first saw Thor1. Reading various comments by my fellow members here and my own inability to tie what we've already seen in the various movies to branches of science made me think I was going to have to let go of that notion. You have some new ideas of how that could yet work, so I'm jazzed about that.
What you're proposing adds several layers of exposition, so Marvel Studios will be challenged to weave the whole narrative in a way that people not already familiar with all the characters can understand. As an example from my own experience, when the rumor first was floated about Dr. Strange appearing in Thor2, I was dismayed to find his page on the Marvel wiki to be about 3x as long as Thor's with a whole army of people I had never heard of before. So part of me hoped that the rumor was a red herring because it was so daunting to think of trying to learn who all these characters are. And I'm one who is trying to become fully versed in all the Thor stories (at least the major ones), and to become at least conversant with other Marvel properties tied into The Avengers. (And I'll make a good faith effort to read up on all these people you mention, I promise!) So I think Marvel will have their work cut out for them to keep the general audience with them. Not that I don't think they can do it, just that it's a challenge.
They will want each film to work as stand-alone pieces as well. Not everyone will see all films, yet will need to be able to follow what is going on in whatever film in which they find themselves.
What you are laying out for us is quite rich in detail, though. We're starting to discuss some of the ideas in the "Plots based on Spoilers" thread, so please be sure to look there too (and add to those plot lines if you so desire)