After having some time to sleep on it...
1) I'm not as furious as the official fandom is, but the sheer amount of unaddressed character plots and ... frankly direct implications that a lot of the main cast just died in the ending are pretty terrible. It's probably not what Hussie intended but it really sticks out, what with how well everything else was put together, that the ending just kinda jumped ship there.
2) "I'll make an epilogue somehow at some point in the future." Gee, thanks? If there was enough actual ending to make an epilogue, why wasn't it in the ending?
3) Something drastic happened to make Caliborn completely uninteresting after his LE transform. The climax doesn't even bother sticking around to see LE's defeat, so even the story CBA to care about the main villain. For that matter, LE and Bec Noir are pretty much the exact same plot: Evil guy with power cosmic is bored and killing everything. Nothing can touch them in a fight, so there's years of dicking around until their distaff counterpart shows up to cut off the source of their power and win the fight (except Bec Noir actually tangles with the main characters more than once and actually creates interesting drama). I liked the Condesce as a villain so much more.
I've seen worse endings, but this one makes me think something happened to it mid-production that disrupted a lot of stuff. Shame, because the animation was really well done for the frog breeding and what should have been the climax.