The one thing that keeps bothering me with MAS updates is that you cannot see the download/install progress.
It will show it at first, but then the progress bar indicator simply disappears after a short time. I have to close the App Store window and reopen it, often multiple times, in order to be able to see the download progress again.
This is not an issue for smaller updates, but larger Xcode updates are a pain trying to figure out how much data has been downloaded so far.
For some reason Xcode updates are shown in Launchpad (both the dock icon and if you can manage to find the app in Launchpad itself) and then sync'd back to the App Store after some delay. The delay seems to be completely random.
I think for some class of updates that includes Xcode and OS the App Store uses a separate tool to download and run the update so it has to use some sort of (very) delayed IPC mechanism. Regular apps update through the App Store itself so it shows progress immediately.