Earlier quoted context omitted.
For the reasons that you've specified and others, I rolled my own very simple sync system based on Git. The biggest problem I personally have with Dropbbox et. al, is that none of the commercial solutions sync symbolic links opaquely . ("Opaque" syncing of symlinks means to sync the links themselves and not what the symlinks link to.) I use symlinks heavily and so I absolutely require this feature. Most of the commer…
Sounds like it's time for a "design pattern" or "best practice" -- that is, covering up for a tool's faults. What if you treat DropBox as a raw, strict hierarchical store and never use it directly, but only link into it from elsewhere? Move all the links outside of it. ln ~/Dropbox/photos ~/Photos ln ~/Dropbox/family/baby/cute-movies ~/Photos/baby-cute-movies etc.
(2) Your suggestion is extremely difficult or impossible to do in the general case.
(3) I have better things to do with my life than rearrange my entire filesystem to suit the ill-conceived whims of a product that does the wrong thing.
(4) I would like to sync parts of my filesystem as they currently are.
(5) I have my own syncing solution that works better for my needs, and it only took me a couple of hours to throw together.
(6) I'm going to use BitTorrent Sync in the future for most of my syncing needs (as long as it turns out to be reliable) since it does syncing properly in the face of symlinks.
(7) I'll still use Dropbox for simple sharing of files with friends and getting files onto my iPad. Apparently, Dropbox just doesn't care about the needs of more sophisticated users, as that isn't a very large market.