Oh my goodness a Transformers piece there. But you make a good point she was trained to eventually take over. And I think the reason most people where mad about it is not because of OP issues but more because we all knew it was going to happen. My friend and I where talking about this and its like Well we knew it would happen so its almost like Hasbro was like well hey lets just end this at 3 because we have sold millions of dollars in stuff. Oh what you say that the Bronies are demanding more? *Looks at the books.* Well then more we shall give. It was probably planned to end this gen of the show and our Rage may have kept the show going. That might be a positive use of Rage on the internet that deserves further study.
As for Balance I don't think there needs to be a balance of pony types because even with the 2, 2, 2 the only ones that where even kind of the same was Rarity and Twilight with their magic though Twilight was always getting better with hers and more powerful while Rarity was comfortable where her magic was. Rainbow Dash and Fluttershy are completely different in how they do things and how they see the world. Fluttershy sees the animals and her friends and cares for all of that meanwhile Rainbow Dash just wants to be the best. The earlier point of Apple Jack and her strength and work ethic mixed with Pinkie Pie's craziness they aren't the same either. So this may actually almost balance the mane 6 out better then the last equation. So now maybe Twilight who can work on her magic and her flying may end up being the one to balance the group more because she can see from more then one view of the group allowing her to be more of the leader if you will in the group of friends. There is some food for thought.