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There's several reasons why you may not find them all that '3D'...

starting with the obvious: it's not 3D, it's stereographic. We still call that '3D' because you get depth cues from it and depth would be the third dimension.

also obvious: when you move your head, the perspective doesn't change. For 2D, your brain doesn't care so much* as it's been trained in seeing 2D images since you were born. Stereographic images however do fool your brain into getting a depth cue, and it assumes that because it gets depth cues, you should be able to get a different perspective by moving your head. This confusion fades after a short while (depends on the person), but it'll always be there. The worst thing is.. your eyes jitter, even if you keep your head perfectly still, your eyes will still be bouncing all over the place - with minute movements, but your brain still expects the minute differences in perspective it's used to from actual 3D environments.

less obvious: you get depth cues of, say, an object being up close... something silly like the sword in Beowulf... right at you through the screen. You look at it, essentially crossing your eyes a little like you would any object that gets closer to you.. but now something funny happens. Your eyes, when they cross, by virtue of the brain will try to focus at a depth of the intersection point of your two eyes*. However, the film is not -actually- 3D.. so you're at the mercy of whatever focus the film's producer decided upon. So if that tip of the sword is squarely out of focus, your brain sits there wondering what the $&#* is going on. This effect is not so pronounced for surfaces further away (much like a focal distance on your camera of 15m will happily cover 14m and 16m as well, and far beyond those; while a macro shot at 2cm distance requires very careful positioning of your camera's distance to the subject to get the correct part in focus... e.g. photographing an insect and trying to get its head, rather than some leg in focus) - but at the same time, depth cues get much less pronounced as surfaces get further away - simply as they converge with perspective.

There's a few other reasons, including keystoning of the projection (when seeing a stereographic 3D feature, try to sit as close to the center of the screen when projected out to the seating as possible), but the above are the main three.

It bugs me as well, but for some movies it's absolutely worth seeing the '3D' version.

* This is also the main reason why some people have issues trying to see side-by-side type stereographic images. Getting your eyes to see a surface at one distance (depending on how much you have to cross your eyes to make the two images overlap), while the lenses of each eye focus on another distance (the display surface) can be unnatural and some people simply never get it happening for them.

For kicks.. close your left eye, now with your right eye, try to focus on a nearer distance (without cheating using another surface). Do the same with the right eye closed and left eye open. If you can do this, you can probably watch side-by-side stereographic images (of the cross-eye method) easily.
Now for your brain kicking in.. open both eyes, and try again. You'll find this difficult at best and impossible at worst - without, in fact, going cross-eyed.

Human visual system is fun - and that's without going into any optical illusion stuff :)