It looks a lot less like BioShock than BioShock did to SS2, and that got a better score, and it further apart.They completely changed the design for AC whilst making an impressive open world.
With this it just seems its Bioshock with different skins and whilst there is nothing wrong with that, I just feel it can't justify a 96 meta rating.
I don't think it's relationship to BioShock is going to make much difference either way basically. I don't think it ever does for sequels, no one cared that GTA4 wasn't some revolutionary redesign of the genre, in fact, it's a lot less varied than SA, and still scored better.