I was wondering the same thing about how slow it is to upgrade too.
We use the _references.js file for helping the JS statement completion. This file dynamically updates as JS files are added to the project. As the KendoUI is updating the JS file, this _references.js file has to be touched to rebuild the JS information. Since there are so many Kendo JS files, it just bogs this process down.
http://madskristensen.net/post/the-story-behind-_referencesjs
To speed things up on our end, we removed the _references.js from the project before running the Kendo update. Then when the update was complete, we added the file back into the project.
I also think you can turn off the autosync at the top of this file before starting the updates. (There is a right click context menu item to turn it off and on too)
<autosync enabled="false" />
Hope this helps. Maybe the Kendo updater can figure out how to turn this file off during update, and refresh it when its done.