There's some parallels between the Android/upstream scenario and Canonical's approach to upstream. Mark wrote a lengthy defence of Canonical's focus on components that they feel need development, while not putting development effort into things they feel are good enough already. That's pretty consistent with the discussions I had with him at the Ubuntu development meeting in Oxford over six years ago. Back then the focus was on taking all the excellent software that already existed and concentrating on providing it as a single polished and integrated product. It was successful - what's easy to forget now is that the first release of Ubuntu was massively more usable out of the box than any other Linux distribution available at the time, and it's absolutely undeniable that its release spurred increased efforts on the part of competitors. But I don't think the same focus is being applied any more.
The most obvious (and most controversial) example is the Ayatana project. Ayatana's a pretty explicit statement that Canonical don't view the existing Gnome UI as being suitable for their vision of the Linux desktop. That's absolutely fine. However, unlike many of the papercut projects, Ayatana is a set of complete reimplementations of functionality that behave differently to their upstream equivalents. There's no meaningful sense in which that's not a fork of Gnome. And, let me emphasise, I don't think that's a bad thing.
Let's go back to Android. While we talk about how much we'd have preferred it if Google had interacted with upstream before implementing wakelocks, the realistic outcome is that there's no way that we'd have accepted them even if they'd been posted years before hardware shipped. If there'd been a productive outcome to that aspect of the conversation it would have involved Android having a very different power management policy. Sometimes you're not going to convince people that something is better without implementing it and seeing how well it works. The problem with wakelocks is not that they exist or that Google feels they work better than the alternative, but that they end up integrated into drivers in a way that can cause divergence between mainline and Android.
Ayatana potentially has the same outcome. At some level, well-integrated applications have to be aware of the environment in which they're running. The application indicator patches are an example of that. Carrying conditional code increases maintenance burden, reduces test coverage and is a net loss in the long run. If upstream Gnome never gains support for this functionality, and if Ubuntu continues to depend on it, then Canonical have a delta that they'll have to carry forever. That benefits nobody.
Forking because you believe that your approach is better is a completely valid development model, but in the long run can cause problems if you don't have a long-term strategy for how to resolve that fork. For all we criticise Google's ability to get Android code into the mainline kernel, they've put orders of magnitude more effort into doing so than Canonical have in terms of getting Ayatana's code into mainline Gnome. This isn't a function of Google's relative size - the Android kernel team is on the order of 10 people. It's not enough of a difference to explain the disparity.
Canonical would be perceived as much better team players if there was an indication of their long-term plan in terms of Unity and the Ayatana projects and getting that code into mainline Gnome and integrating with the Gnome shell. It's completely unsurprising that they're viewed with distrust until that happens.