A friend of mine did this to a very high standard. He is a professional editor. Even the quality of the discs themselves, the menus, the box cover - everything was done superbly (with, perhaps, the exception of 5.1 sound). The music, by and large, was easy to mix from one scene to another or just gently faded out.
The result really does work. He used my timeline and a chronological source
http://www.tiki-toki.com/timeline/entry/5395/A-Marvel-Cinematic-Universe-Timeline/
It's on 5 discs of roughly 2 hours each. Finding the points to swap from one disc to another was a bit of a chore to make it work narratively. As is certain days when a number of things happen to make it make perfect sense.
Some of the bigger arcs and larger stories really come to life. Howard Stark, the Arc reactor, the tesseract, super soldier serum all have a deeper meaning.
On top of that some scenes by pure chance seem like they were pre-planned by Marvel (although they weren't) One example is when Foster, Selvig and Darcy are chatting on top of their research centre bemoaning SHIELD interferance at taking all their equipment. Selvig mentions that a Gamma scientist 'bumped' into SHIELD and was never seen again. We then cut to Banner cycling through Culver University delivering pizza.
Also near the beginning you cut from the Jotuns invading Tonsberg and the Asgardians driving them back - the next scene is Schmidt showing up in Tonsberg and taking the Tesseract.
Was a great way of leading up to my viewing pleasure of The Avengers.