I remember going on numerous blogs on places like Gamasutra and people were constantly shitting on it. Every time it was brought up in any sort of discussion regarding game design, people were on the ready to shit on it. I honestly can't remember just a few specifics because it happened so often.
It got a lot of flak for the game design because (very specifically) the
game design is somewhere between "bad" and "perfunctory" on the general scale. The environments are a succession of combat arenas designed for 8-16 enemies (you may replace 3 enemies with an "elite" or 6 enemies with a "miniboss" as needed), 2-3 means of navigating them (at least one of which will always be skyhook), and 2-3 spots where Elizabeth can magic up a cut-and-paste environmental asset like a cover element or turret. These arenas are separated by very brief traversal sections that mostly just seem there to give Elizabeth a chance to do cute things and are rarely fun or interesting to explore, since they almost never make a difference in how you're going to arrive at the next arena.
That's not even getting into the abysmal boss encounters.
It feels very much like a game built by artists where the game design was an afterthought, probably provided as a cookie-cutter "template" (ala Skyrim dungeons) that a non-designer could hew to fairly easily without input. I'd say in that regards it's basically a (much better) version of The Order: 1886.
Note that this is about game design--level design, encounter design, game mechanics, etc.--not about dialogue, aesthetics, world-building, etc. A game can have horrible game design and still captivate people, but it is relatively odd in this case since BioShock's game design, while perhaps never
amazing, had never felt so... tacked on.