To me too innocence felt like it was a lot closer in style to the first GITS movie than SAC, it has this more philosophic and artistic approach, whereas SAC seems to rely more heavily onto the dialogue and plot. It has a certain art movie-feel to it, and while there's some quality GITS/I.G action scenes, it's maybe not as 'entertaining' as the series.
I must say that I also didn't like too much about the first movie, and as this second one seems to be more like a remake or tribute to it (it's awhile when I last saw the first GITS but I think there's at least a couple of pastiche scenes in innocence) you need to take my critique with a grain of salt -->
It just felt like innocence was lacking story-wise, and dialogue and ending seemed a bit forced to me. (the dialogue was maybe a bit off anyway because of imperfect subtitles) In graphics department, 3d art and effects were top-notch, 2d animation was usually good but there's some points when it was a bit jerky. More frames or a bit of motion blur would have been nice.
Maybe I was a bit tired and didn't catch all the 'hidden' meanings at the first viewing. I may want to give this kind of movie another try. It's not that I have to force myself to do so, as even with it's some shortcomings, I still find innocence to be a beautiful and stylistic piece of animation.