It's definitely the tech getting in the way of the experience. There's comments to be made about the gimmicky nature of content made for 3d but if it really took off you'd eventually see stand out art and ultimately it would become so standard and expected that even for a film not taking particular advantage it'd probably be there, literally, adding another dimension to the experience of the film. The problem is, in all it's history we just haven't figured out a way that isn't clunky and irritating on the viewing side. A pair of plastic glasses may seem a pretty minor inconvenience but people balk at that type of thing and only have the desire and patience for it during brief spikes where it re-emerges as a fad.

It also, from memory suffers from making the films seem darker, the glasses are prone to being lost, or scratched. To make them comfortable you'd really have to make them as good as actual glasses, which are expensive. It's also problematic from a theatrical perspective because a session has to be 3d only, you can't have people in the same session watching it without glasses, the screening is unwatchable without them so you have to tie up 2 screens with a 3d and 2d version. I think I recall hearing about advances the last time this fad was big, where they finally didn't need glasses, but it resulted in narrow viewing angle requirements.

If you're picking up a theme here, it's that all the complaints are about the practicalities of the tech, not necessarily the entertainment value of 3d itself. The trouble comes when that entertainment, while fun, isn't worth it.