What are the disadvantages? Uh. Ha. Well, speaking from experience:
1. The glasses aren't always clean. One time, I couldn't even use them, the movie looked LESS blurry without them. And I tried to clean them. Like, every 5 minutes. Because I was watching a blurry, 2-D movie and I didn't have much else to do. Didn't help at all. Believe me, if I could've cleaned them, they would have been cleaned.
2. Hurts my eyes and head after a while. I have to periodically lift them up and give myself a break.
3. It only works for a very specific kind of shot, and ruins others. Look at Prometheus: The opening shots of Earth are fucking astounding, as are many of the really wide "eye-candy" shots. But when it's just a bunch of people with a big, complicated hologram thingie in the middle? Totally ruins it. Everything gets blurry whenever the camera moves too fast, so it's impossible to focus on anything. Plus, the blurriness just adds to my head/eye pain. But the hologram just looks SO COOL I guess it's totally worth it.
4. I know this isn't inherent to 3D effects, but LOTS of filmmakers and studios tend to abuse it. I have a feeling that's what MOST people are talking about when they complain about 3-D. I'm sure there are a lot of people who actually aren't bothered by the effect like I am, but dislike how it's currently being used: As a cheap cash-cow with (somewhat ironically) no actual substance.
5. After reading the OP, I'm not entirely sure we're watching the same 3D movies. The OP seems to be under the impression that stereoscopic 3D effects can mimic an actual 3-dimensional space flawlessly. And it can't. It really, REALLY can't. I mean, sure, 3D is great in theory, but the technology just isn't there yet.