It makes perfect sense and I'm pretty happy about it.

In the earlier days of WordPress MU it was a complicated installation followed by complicated management. WPMU has proven much easier to install and manage over the years and some of the bug fixes to WPMU went directly the WordPress Core.

Basically the code that makes WPMU work has been getting smaller and more compartmentalized, so I could imagine that the effort to maintain a WordPress Fork for Multi-blog functionality starts to become a huge complicated waste of time. With a merge you can have Donnacha and the WPMU community working with WordPress Core. So instead of reporting a WPMU bug or feature and finding out it needs to be reported to WordPress Core you just report the bug in one place. Nice!