Ok, let me try. I spent a little time on this question with the writers while working on Marvel's Avengers Black Panther's Quest (Premiere 9/23, this Sunday on Disney XD). I think that like with the comics, some stuff should be open for interpretation. It's up to the reader or the viewer to decide how it fits best in his or her head. That's always been part of the fun for me as a comic book fan. If it works best for you that each show has its own continuity and that each animated series is an adaptation of the comic book material in its own right, with shared elements across shows, then that's perfectly legit. If you believe each show is in a shared continuity and you have a particular way that all those puzzle pieces fit together, then go with that! The essentials of who Marvel characters are, that all comes from publishing, and that really doesn't change very much. But the visuals and designs do change in animation just like they do in publishing when a new artist comics on a book.
Now all that being said, having been in story summits for all the animated shows, this is the way that I PERSONALLY look at it. Ultimate Spider-Man, Hulk Agents of SMASH, Avengers Assemble S1, S2, Ultron Revolution, and Secret Wars all live and work together for me. And Guardians of the Galaxy, Marvel's Spider-Man, and Black Panther's Quest all live and work together for me. But that's not to say that a very close version of the storylines that happened on Avengers Assemble aren't still viable on Black Panther's Quest. For example, on Black Panther's Quest we'll be continuing the Whitney Frost/Hawkeye storyline we started during the Season 4 Halloween Special. Black Panther's Quest may live in a different continuity for me from Avengers Secret Wars, but that doesn't mean that that story, or a very close version of that story, didn't happen in both continuities.
Here's the fun part…in the last season on Avenger's Secret Wars, Beyonder brought worlds and realities and continuities together but when the heroes won, maybe all the pieces didn't get put back together the exact same way???
Short version: make your own theory, put the puzzle pieces together the way you want to, don't let anyone tell you are wrong, and have fun with it!
And check out Marvel's Avengers Black Panther's Quest on Disney XD this Sunday!