In reply to Mark.

Custom Logo was also part of Jetpack first, and got integrated into Core later.

I too, think it would make sense to include this in Core. However, I can see the advantage of adding it to Jetpack first, figure out how it interacts with most themes out there, fix bugs, make it easier to use and integrate into themes, ... Then, once the product seems stable enough, propose it for integration into core.

Consider it a Beta period of sorts. :)