The Forum kinda kicked around some ideas about whether and why vintage April was being intentionally banned form merchandise. The Big Bad thought something was up, and I kinda thought such speculation was ridiculous (April rarely featured prominently in vintage Mirage TMNT art), but once the news of the variant cover edit came out, I had no choice but to admit something was unusual:
http://forums.thetechnodrome.com/showthread.php?t=47293
I'm still more inclined to think Nick discourages featuring female characters on covers since there's a long standing corporate assumption that males/boys of certain target demographics don't want to buy stuff with girls on them, but Renet and Ninjara have both made appearances since then. Maybe they think vintage April looks too boring? On the other hand, Nick April has already been featured on at least three covers (more if you count all the variants) for the current New Animated Adventures comic.