I can't tell you much about Android tablets, I've never even seen one myself. But there is a review on Ars Technica of the Nexus 10
that says the tablet is good, but the Android market is weak. So I guess one big advantage of iOS is the Apple app store, and the apps are what makes a tablet good at syncing or reading various formats.
There are several apps that allow you to annotate using the keyboard. iBooks is one of them. It reads PDFs and ePub and syncs between iOS devices. The Kindle app also allows annotations but only reads mobi. It syncs with more devices, but the syncing works best with books bought on Amazon.