Unfortunately, the business execs didn't (and still don't) want to lose their precious brand name, and they are still mentally stuck in the Animation Age Ghetto (cartoons are funny animals that are just for kids).
I believe you are correct. It would seem that with the popularity of the more adult (and I do use that term loosely) versions of these shows, they would continue to create them instead of trying to make cartoons for the kindergarten kids. Or at least make both.
Do you think Wally would start to believe he is Reverse Flash? The reason behind my asking such questions like this is because, season 3 to me felt like it was going to be much darker in stories, what with Darkseid and all. I thought we might see some of our heroes turned evil (possibly for the season), and then turned back to normal again.
Let me be honest here, if there was a third season, we would've saw change (not red wedding change), the kind of change you'd expect from something that happens in season 3. Because to me, season 3 is the season of change.