I also notice that the "hotplug" functionality is not always as stable on the latest rom. If you turn on your MOJO make sure that the HDMI cable is attached. Sometimes if you plug in the HDMI after you turn on the MOJO - sound could be lost. rebooting solves this in my situation.
Yes to be fair this also happens with the Raspberry Pi. If your TV isn't on or the HDMI cable isn't plugged in when you switch it on, you'll get nothing, even after you quickly plug the cables in/switch the TV on.
The main limitation is that the apps on AndroidTV need "leanback" support. Very simply said, they must be easy controllable with a "controller" (not mouse/touchscreen).
So on the Playstore you'll only find app with leanback support - which is represent ? 1 - 10% ? of all android Apps.
You still can side load all non-leanback apps on the AndroidTV rom but once you start using the "AndroidTV remote" (for me a keyboard/mouse on the mojo doesn't make sense if your on the couch :/) You'll feel that you need a leanback-app to have smooth control.
Beside this there is practically no difference.
Hope this gives you a bit more insight.
Ah, now this I did not know, so thank you for the information. I always admired the Android TV interface and thought it would suit the MOJO very well, but I did not realise it came with these limitations. I suppose it makes sense in some ways, but I would be very upset at losing so many apps and I wouldn't really fancy having to sideload so many.