The nature of dropins is that they were supposed to be a transitional mechanism between old update manager and P2. Dropins have more advantages that they were supposed to have, and one of them is truly easy management - just copy a plugin, and it will work (in most cases).
This time, however, a really nasty issue managed to get into Kepler. It was discovered about two weeks ago, when some of our Fedora packages started disappearing after updates.
We often get similar issues before final build of Fedora is released, so it did not looked seriously. But after a couple of days of checking our build process and testing I've found that:
If you deploy into dropins a plugin that is already installed using P2 director, your Eclipse goes bananas, especially if this plugin is a platform dependency.
The dropins mechanism will try to uninstall it, and then, depending on your configuration, will stop working, or will break your Eclipse.
The bug was reported in the Eclipse bugzilla, but it will most likely be shipped due to the bad timing in which it was discovered.
So beware of what you put into dropins - unless you want spend the same amount of time that I did trying to understand what's going on.