All notification emails are now hooked instead of plugged. To put it simply, for example, you can now remove the entire comment notification function and replace it with a custom one. When I was in Israel in June, I was posting pictures and getting comment notifications that were not useful.
I have 2 other related tickets with patches submitted that missed the 4.4 deadline I’m hoping to get into 4.5. One deals with more changes to parts of the comment notification system that date from early WordPress to allow the functionality I was trying to get. The other deals with allowing customization of pingbacks.
I also have a few more tickets that are still not ready for a release, but I hope to someday get solutions in for. Several involving the commenting system, and the rest involving semantic markup.