Some voicing their concerns about 3D ruining their enjoyment by giving viewers headaches or disorienting them with fading transitions, wipes and other common 2D movie tools need to understand that there are already techniques in place to remedy these problems.
First off, the new polarization techniques don't use the older, vertical/horizontal polarized light filters. Instead, clockwise/counterclockwise spiral polarization is used, resulting in less image bleed-over into each eye. Second, directors have the ability to lessen the perceived depth of a frame, making it seem not as if you are viewing reality, but more a bas relief sculpture. This helps during transitions or fast motion to keep people from getting headaches or experiencing vertigo. The recent film Monsters vs. Aliens used these variable depth shots quite a bit. I've had problems in the past myself with watching polarized 3D films, but have no problems watching any of the new 3D tech.
I'd say a much bigger concern is going to be how films done in 3D transition to DVD/bluray. If directors start shooting their films differently in order to take advantage of 3D imagery, how much intention will be lost when the film is converted to 2D? Imagine a director tweaks the depth of everything in a shot to lie in the far background, then pulls one particular item forward to emphasize its importance in the shot. Everything else considered equal, that information will be lost in the 2D version. It's a comparable problem to taking a color film and turning it into black and white. If "the girl with the red umbrella" suddenly becomes just some other person amidst a sea of other gray umbrellas, the meaning of the shot is lost.
Some newer TV's have 120hz refresh rates (or better) to allow for 60fps stereoscopic imaging when using shutter glasses, but that is hardware which is going to have a hard time making it into living rooms.