First of all, it combines two narrative 'tropes' that I really don't care much for at all. First would be "nukes" in a nutshell. Yeah, in a pseudo-future show like GitS, nuclear threats aren't unreasonable at all, but I still find it to be a lazy, cheap, boring, most simple way possible way to sets the stakes high. More a personal taste thing than anything, it's simply not an interesting primary impetus for the main characters. (I also don't like that the whole overarching Robin thing in One Piece seemingly boils down to "nukes" either.) Second is when an antagonist character's endgame involves a type of "new human evolution". Perhaps more a JRPG thing than an anime thing, this trope is so overdone, vapid, and vague. In this case, it was a more minor point than main goal - still rolled my eyes hard when Kuze started spouting this nonsense.
More problematic though, is how overstuffed the climax feels. You have several different storylines tying themselves up in an exceptionally cluttered fashion. You have Kuze launching his 'revolution' and how Gouda fits into that, the friction between Section 4 and Section 9, Kuze and Motoko's relationship in a past life, the Prime Minister's struggles in heading her cabinet, the Tachikoma's forming a sort of consciousness and sacrifice, even a sudden random inclusion of a new prototype bio cyborg that seems superfluous to everything else.
I might sound like I'm whining a lot - there were still a number of scenes, stand-alone (hah), that were enjoyable in a vacuum. Some of the chase after Kuze scenes & the final confrontation with Gouda for example. Despite all the messiness, it manages to be somewhat enjoyable. But overall, things come to a head in a very manner that's not very well constructed.
