I'm confused why someone would want to run the decidedly hamstrung version of Wordpress if they have the option to run the "real thing"?
For example, Wordpress.com blogs do not allow JavaScript of any kind. They make decisions like this to better be able to handle the scalability of their hosted offering, and for that it's entirely logical, if not a bit annoying.
Would the Jetpack version of Wordpress be similarly locked down? Of course you could make tweaks to it to do whatever you want with it once you host it on your own, but then again, why not just use the full wordpress.org version?
Open-sourcing a few plugins that were previously only available to Wordpress.com users would be just as nice, but I guess then the ability to put the word "cloud" in big type doesn't fit as well.