It looks like Youtube is phasing out the ugly (but useful) annotations to make way for 'End Screens'.
As far as I can tell, the main reason for the change is to make your videos more clickable on mobiles. Annotations do not show on mobiles, so with this change you should see a lot more interaction. However, you can only place the new End Screens in the last 20 seconds of your video - hence the name. So people will need to be watching your videos to the end to get any clicks
The positioning is also quite limiting compared to annotations, as they must fit inside a blue box that's placed in your video (only in editing), and some of the screens are quite large, even at minimum size - and some of the screens cannot be resized.
That's my first impression after just coming across it, has anyone else used them yet? What do you think?
You can read more about the change here: https://techcrunch.com/2016/10/26/youtube-launches-mobile-friendly-end-screens-feature-to-keep-viewers-watching-more-video/