@Fracture: You're right on track again, as far as I'm concerned. I love highlights, but I, too, was hoping that they would be able to be added on different parts of specific images, rather than simply linking to the whole image.
I know that I would much appreciate a longer space to type information for such detailed highlights and being able to insert links to external sites would be a huge plus. I know that the main concerns are that spammers would begin linking people to whatever spammers link people to and that people would ramble on too lengthily, but I think that making honest users suffer in order to avoid people who misuse things from spamming Photosynth is not the right direction.
As far as placement, I'd like to see a panel extend below the bottom of the viewer for any/all annotations with the borders of the highlight simply snapping to the borders of the viewer, leaving the image unobstructed. This would also solve the slowdown from text atop images.