The second seasons of Mighty Avengers does something quite interesting in terms of comic continuity, in that it takes various plots from the comic source and then reverses their chronology (first Secret Invasion then going to the home world of the Kree). Compared to the first season this season also feels a bit like Justice League Unlimited, in that instead of concentrating on the core group of Avengers, more and more others heroes are introduced in an anthology-like manner.
My biggest beef with the first half of the series is probably that I really dislike the whole Secret Invasion era, mostly because I have a big hate for any plots that rely on some of the main cast being doppelgängers, shapechangers or similar stuff. Especially when that sub-plot is going on for what feels like forever. Another problem I had with the second season was that it felt like the animation was often subpar when compared to the first season. And the re-cut intro with the horrible voice over didn’t entice me much. And that Wasp is still portrayed as the most useless team member, despite having better powers than some of the others just feels troubling (not to mention the awful costume of Ms. Marvel).
Still, all that said, seeing classic Avengers plots streamlined for television and thus freed of all the extraneous continuity fat was fun in itself. Stupid fun, but fun nonetheless (I get the feeling I say that far too often recently, there’s definitely a lack of smart fun in my diet). Also seeing Doctor Doom done like a smart evil super-villain instead of a raving madmen was enjoyable.