So I've been using Moodle 2 for about a week in a live environment at Leeds City College and here are some thoughts.
Assigning Child and Meta courses are totally different, there is no longer a "Child Course" link in the Admin menu, you now have to goto Admin > Users > Enrolment Methods and add a course link. Finding a a course to link too has also changed, it's all in 1 long drop down list odd at first but once you get used to it, you'll see that it's actually faster and easier than the previous method
I miss the Related Courses block, I'm not sure if the 1.9x version is compatible with Moodle 2.x yet, I'll have to investigate. (On further investigation, the Related Courses Block is kind of not needed any more, you can see all relationships within the Enrolment Methods option)
All our custom pages have been successfully transferred into Moodle 2.1, this was surprisingly simple.
Changing core icons in Moodle 2 is a pain, you can't just simply right click and view location and override the file with a new one any more. I have read that icons can be changed within CSS (This would be ideal for us) (Info Here)
I totally love the new way Moodle 2 Assigns Roles, this works like a dream.
The Settings block has grown on me, I wasn't too keen at first but you soon realise how powerful this bad boy is
I miss being able to save directly to the Moodle server course directory but I do appreciate why there is a global repository. In Moodles defence you can set up a custom course repository just for that course where you can then drag files directly from the computer to the course.
I love the Duplicate Resource button, this will be a huge time saver for me and teaching staff, gone of the days where you have to sit there and create 30 individual assignments.
Overall I'm pleased that we've made the Jump to Moodle 2.1. We're done, it works and all these little tweaks and niggles will no doubt get ironed out as soon as the academic year progresses.
Did I mention that we are now 100% core, everything has now been modified in the Theme. :)