While Thaddeus' answer touches on the generalities of why Banner wouldn't show up, I think there's something more specific about what's happening in the Avengers Assemble series.
Avengers Assemble takes place in the main Marvel continuity, which is alongside writer Jason Aaron's current take on the Hulk, happening every month in Incredible Hulk volume 3. A quick blurb from Wikipedia about that series states:
At the start of this new series,
Hulk and Banner have somehow become separate entities. The Hulk has
been living as a hunter for an underground tribe of Moloids in
Subterranea while Banner has become a deranged scientist living on an
island and conducting experiments to try to re-trigger his
transformations into the Hulk.
And spoilers for those who haven't read the current issues:
The storyline concludes with Banner being destroyed in the blast from his new gamma bomb, but the Hulk's close proximity to Banner when the explosion occurred resulted in Hulk and Banner becoming one being once more, with their previous existence reversed; now Hulk is the 'dominant' personality, reverting into the criminally insane Banner when he becomes too calm.
Regarding other mysteries that have popped up in the book that also seem to contradict previous stories and established continuity, Bendis stated on his Tumblr (WARNING: that link spoils the ending of Avengers Assemble #4) that the series is:
100 percent cannon [sic]. all will be answered and revealed in story
That means that Bendis intends for Avengers Assemble to be in continuity with the other Marvel Comics, including Jason Aaron's Hulk. Tom Brevoort, Avengers Assemble editor and longtime Marvel employee/aficionado, stated in an interview with CBR:
Tom Brevoort then explained the goal of "Avengers Assemble" in terms
of greater Marvel continuity. "It sits right at the forefront of
Marvel continuity," he said.
Bendis even says in the same interview:
You don't have to mention every single thing that's happened to these
characters to get to this place, just enough to recognize them. Just
don't do anything to contradict continuity.
So given the above quotes, it's fairly evident that Bendis is aware of what Jason Aaron is doing in the main Hulk book and is keeping Banner out of Avengers Assemble so as to not contradict it (or to contradict it less, as I'm not sure how Hulk is being characterized in his solo book). And given his above Tumblr quote regarding the other continuity-defying plot point in Avengers Assemble, it's entirely possible he will address the Banner issue in the future.