You're right, it hasn't changed much...When editing is turned on in 1.9 in a category, it is just check, click the right course in the drop down at the bottom. In 2.5, manage category works the same way.
What's changed is the edit settings page for the course. In 1.9, when the edit settings page opened, by default it selected the first field (I experienced this is both IE and Firefox), so if you wanted to change a setting further down on the page and weren't paying attention, you hit page down and it would change the category. You might be irritated that it didn't page down but wouldn't notice what DID page down. And then later, screaming and wailing and gnashing of teeth ensued.
I think I did this twice, before I started paying attention. But I have several facilitators who couldn't remember to click off the drop down, "accidentally" moved courses on a weekly basis, couldn't be bothered to do a course search and expected me to clean up the resulting mess. Hence, no more permission.
In 2.5, though, the category field is in the third or fourth position on the page, so you can't hit page down and mess stuff up. You have to do it deliberately.
On to your question...I've compared them and I don't see anything amiss...but I might not, since the permissions stuff has changed dramatically, with so many new options (for the better, though I'm always amused when I find depreciated roles in 2.5). We didn't upgrade our old site, we started fresh...did the way facilitator permissions apply to changing course categories change?