I'd be willing to bet the new show will be superior, and the whining over the demise of EMH is going to look pretty silly when AA debuts.
I'm willing to bet that there is a good chance it won't be better, unfortunately. Jeph Loeb is in charge of the cancellation/new show and wants to make something more along the lines of the silly Ultimate Spider-Man show. Loeb was once a mighty storyteller, but much of his experience in TV has been rather lack-luster.
Although I had my qualms with the animation/character designs at times (Wasp's hair), I really enjoyed the writing and storytelling. Not only that, but the show was a great mini-Avengers-history-lesson and hit a lot of great points throughout the first season.
Most importantly, people really liked it and followed it, which like others have said helped to prepare newcomers for the film.