These are many questions and should really be asked as such. But I'll provide a generic answer anyway.
There are heavy underlying changes in 11.10, following the switch to Gnome 3. Theming has become much easier, because it's now just CSS, which is the same as all websites use to define looks. This means that a lot more people will be able to make themes, so we should expect to see some dashing ones in the future. Unfortunately, this also means that old themes do not work.
Themes are just one of many things that have been upgraded in Gnome 3 and hence Ubuntu 11.10. The configuration system itself is one of them, meaning that some settings are no longer available and that new ones have been added. Startup applications is one area that have been changed to become more user friendly. Applications can choose if they should appear in the list or not, for instance. This reduces unnecessary clutter.
This is a large upgrade, much bigger than anything in Ubuntus history. In fact, there's been no change like this for over ten years, in case you joined Ubuntu in 11.04 and think it's a little unsettling with so big changes. They happen very rarely, and you can expect to not see changes like this for many years. It has been very important to get this done now because of the LTS version that is scheduled for April and will be supported for a long time and sold with new computers, etc. Because of that, some thing may be a little unpolished and there are some rough edges still. The good thing is that all the technology is now in place, and now it's time to polish and fix minor issues.