The limit isn't vsync, or the PC, it's just that the current version of HDMI can't pass that much video data. It's too bad, but that said, 720p 3D is nothing to scoff at, and quite unlike 720p 2D. Afterall, you're seeing two different 720p images at once, each with a unique view of the scene. Personally I think 720p 3D is much better than 1080p 2D, but it does come down to personal taste as they each have their advantages. 1080p 2D offers more fine detail thanks to the smaller pixels. 720p 3D offers more unique details, as each eye is getting details that the other eye can't. And, obviously, it's 3D instead of 2D, which is an improvement besides all that. In any case, they're both roughly the same number of pixels, 1080p 2D is 2 million pixels, 720p 3D is two different 1 million pixel images.
1080p 3D does exist though, you just can't get it yet on a standard 3D TV. There are computer monitors that allow that resolution (by using dual DVI instead of HDMI).