The main purpose for these new changes was to make it easier for everyone to quickly get to the most important places, like Forums, Photos, Groups, My Journey, MYOH, and your Settings. On top of that, we made the whole navigation flow and feel a lot faster (which I hope you've noticed!).
We realized that Meebo was really not being used much, so it's not worth having those popup ads on your page from something that's rarely or never used. Also, it would constantly keep connecting with the Meebo servers multiple times a minute (that's just the way these chat clients work), slowing down the site in the process. All that overhead for something that's not really used? So off it went!
The other aspect regarding the bookmarks, in addition to what was said in the main post, is that it was built a LONG time ago using some REALLY old code, and it was simply not going to work with the new smoother navigation. But as mentioned, we're working on a way for you to at download your old bookmarks, so stay tuned for updates on that.