Now with the BitTorrent Sync version for mobile, DropBox and Cubby are almost obsolete. The only thing that is missing for a range of infinite apps is scripting or an API, those would make apps so easy to develop, including web interfaces, p2p message communication, and so on.
I do agree that the current solution is not scalable for a huge number of files, I was having problem with that (high disk usage and trouble with Windows Index Service). However using a purely file system based store is the most compatible way to write any storage system. I would say that porting to Android is a priority, and leaving everything as a file system based store is the best option now. Nevertheless, I do hope we have a faster way to index faster in the future.