The first issue is that iCloud restricts syncing, and thus your application, to iOS and OS X devices exclusively. This probably isn’t much of an issue for many, if not most, kinds of applications that will only ever be on iOS applications, but for others, choosing to use iCloud places an unscalable wall around the application’s data because iCloud offers no way to access the data it stores from the web or other, non-iOS and OS X devices, at least for now.
It’s a point I never really thought about at all. Dropbox is universal across platforms, and iCloud isn’t. I am sure that a majority of people who would use iCloud are Mac only users, but if you go with it you are committing to that assumption. It will be interesting to see how many apps take this into account.