It's a retool. New title (because they had to use "Avengers Assemble" for the UK release of the live action film anyway). New art style. New VAs. But the characters still remember the events of the past two seasons.
As someone who doesn't read comics, I really enjoyed the two "Earth's Mightiest Heroes" seasons. I don't know how closely it follows the comics, but as a stand-alone it works really well. My only two complaints are the season two intro sequence (which ditches almost all of the cool theme song and adds a totally unneccessary narrator emphasising that the heroes who have had recent live action movies are indeed in this show) and the fact that season two starts to add a number of extra heroes who are so powerful it starts to unbalance the group a bit, leaving me feeling like some of the others (like Hawkeye) haven't really got anything to do. Otherwise it was a really strong show.
They do constantly juggle which characters are in the roster at any one time though, so you have to like a number of them. If you find you only like (for example) Iron Man or Hulk, you might be disappointed when they disappear for several episodes at a time.
