I've long wrestled with this idea. I was 14 when it came out, with it's impressive visuals, an actual attempt at a story and lavish praise, I accepted it as one of the best shooters of all time. I've gone back and replayed it recently and I'm not sure if I really like it. Or, if I even liked it back then. Today, I do have to give credit for Rapture being a consistent, believable overworld (and I loved the plasmids), but the GAME just wasn't really fun (or as insightful as it tried to be).
Reasons why I (personally) feel Bioshock is overrated:
1. Overwhelming. It's claustrophobic, maze-like and overstimulating. This is more of a degree of personal preference, but the world didn't make me feel insane after a while; it just made me feel annoyed after a while.
2. The combat. Instantly regenerating without a real death penalty makes the game too easy and let's you win by sheer persistence. Big Daddies were really durable, but not threatening as a result; making the battles with them tedious.
3. The story. Yes, it's better than the majority of videogame stories (because they suck), but if it ever tried to be a movie or novel, it would be average at best and laughable at worst
4. The political themes. I was impressed by games taking on political and social themes, but as I got older, I realized that the game just threw provocative imagery at the screen without a real message. It talks about genetic modification but doesn't pursue it any further than that. The only opponent Ken Levine took on was Ayn Rand (who I definitely wouldn't consider a worthy one, or one who needed to be refuted). 99% of us already knew she was a looney.
5. Fetch quests. Yes, the game was story driven, but most the things you actually DID were just fetch quest. Collect X, Y and Z. Then walk to point A, B and C. And shoot lots of enemies along the way. Much like Arkham City and Red Dead, what you actually did in the game just felt like filler in between story points rather than part of the actual adventure.