One thing that Genndy mishandled for sake of storytelling (which was rather bad in my opinion) was Ashi disappearing - killing Aku would mean that Jack would not be able to get back, grandfather paradox and the works, Ashi should've disappeared the moment Aku died or not at all.
The "bittersweet" in the ending is just shoved in our faced rather badly, as opposed to flowing out of the ending, because it was "too perfect" in how easy it was, but I think it was the problem of pieces present for the ending's resolution as opposed to the writing or situation presented. Without this happening, the ending would not end in anything other than happy, which at this point didn't really make much difference and is quite jarring to have such bait and switch after happy notes of the season - the contrast is just too sharp.
It jars with the start and the first episodes as well, but the tonal shift in itself is not bad if it portrays something and I think this season did it rather well, from despair to hope. Ashi disappearing where she did (as opposed right after Aku's death or not at all) is just unnecessary and cheap.
7/10 from me, Genndy.