I am a long time Apple fanboy, really love the iPad. But honestly, I am starting to get annoyed with some missing customizations that Android has had for ages. Not talking themes.
For example: Intents. iOS 6 looked like Apple was headed that way with the way you share pictures or links. However, only a few select companies are integrated with it. I want to be able to add a screenshot right into Evernote. Use a different "read later" provider. I use Chrome on the desktop, which doesn't integrate with iCloud reader. Same thing goes for bookmarks. I use xmarks for syncing across multiple machines and I primarily use Chrome. Xmarks is also awesome for having work profiles. iOS xmarks integration is very limited because of Apple.
Widgets: I can't believe that after all these years of widgets in OS X they haven't brought them over to iOS. It would be very nice to have a dashboard for lets say system status at work. I don't want anything too abusive on system resources, but allowing one of these widgets to update in the background or via notifications would be awesome.
I was honestly considering picking up a Nexus 7 once the LTE version is announced. The announcement of factory images for the Nexus 7 has sealed the deal for me. Will I customize it to that level ? Not sure. But I would like the option.