On the contrary, it's the perfect sequel by not trying to be GITS 2.0, and instead, making the story about Batou rather than Motoko Kusanagi, who was not exactly in the best position to be central to the story. The story actually makes sense, it's not a facade nor is it pseudo-intellectual.
Spoiler
Little girl has soul stolen, starts wreaking havoc with the dolls so that someone figures it out and comes to save her. Batou does, the end.
I will give you that it's a "difficult" movie, and I have to admit, I didn't get it on the first viewing, so you're really in no position to criticize the story if you don't understand it. You can criticize the movie for being difficult, but you can't criticize the story for being non-existent, that's just...incorrect.