My 2 cents...
1. The health bars are more difficult to read. This makes it harder to gauge healing, specials related to health, and just basic attacks. This needs to be fixed.
2. Combat takes too long...I like the game and spend money on it, but I can't spend all day on it. This affects EA's revenue as well. I simply haven't had the need to buy crystals because I haven't had time to use them.
3. I had no issues with the challenges, but I have a balanced high level team with lots of toons. It would have been better to add "hard mode" or new tiers than make it that much harder on existing tiers.
4. In my opinion the game dynamics changed alot....too much. The game went from fast paced high scoring baskeball to slower paced lower scoring hockey. Imagine if the NBA changed the rules so drastically...what would happen to their fan base... I won't stop playing, but the game has lost some of its "thrill"...that was ebbing anyway due to repetition
5. Overall, I think that the game needs more content. I played "Assault Team" before Heroes....the latter is certainly more diverse, but the other one had stories...made it more interesting in some ways.
6. Final thought I understand that the speed meta was an issue.the problem was that there were too many high speed/high damage tools on a team. Maybe the answer was to somehow add structure to team compositions and enforce more structure around the speed and damage associated with each class of toon.