TMNT as a whole has a problem with absent mothers...I'd almost say worse than Disney
.
April's heritage is an obvious problem, and that really could have been handled in part with breaking the Kraang hive mind and delving into the backstory of the Council and scientist Kraang's betrayal. Especially with Knight going Anakin Skywalker on everyone.
I'm not saying that being an Utrom person (exclusively), but because I think it could have been really, really good material to cover. Especially with the Kraang being the first Utroms that I started to enjoy.