OK. I have to jump in here. Maybe you can correct my mistakes.
I also had started a thread about the same thing. I was moving to another host and thought that would be the perfect time to start up domain mapping rather than site manager. I have a main site, which really isn't anything but the main domain that is being hosted. I am hosting 2 of my own business, a personal site, 4 personal sites for my kids and friends, and one for my oldest son, who needed sub.domains.
I was a little nervous, because domain mapping is in early development and Donncha mention's something on his site about 'remote login' being a problem, but I never understood what that meant.
I decided to leave my businesses alone, and leave them on 'sites'. I also setup my older son as a site because he wanted subs. I then setup my personal site as a 'site', but stuck everyone else as a blog under my personal site and used domain mapping for those. Thus, making my personal site really a true WordPress MU model.
Everything was fine, but then strange things started happening. I would be cruise to sites just browsing the web, see thing I would want to change for their sites, and go into the admin area. I would then start getting messages saying I didn't have permission while in the admin area. This was strange since I was the site admin and very confusing. Was it the remote thing biting me?
I finally figured out that I needed to go back to the main 'site', my personal site, and go to Site Admin > Blogs > Backend and then I could do anything. But if I forgot this, I would sometimes start getting the errors.
The other sites, my kids really don't do much, so everything else seemed fine. But when my middle son decided to start working on his site, he also started getting errors that he couldn't do things even though he was the blog admin.
So I finally moved him back to a site from a blog (which was not a joy to do but I would be happy to start another blog on how to do this without editing any of the databases). He now can do what he wants.
My oldest son wants subs so he can start hosting his friends domains using domain manager, but I am now worried he is going to run into the same problems that I did.
So, what are the 'real' limitations of a mapped domain? I wish I could tell you. What I do know is if it is a 'site', I have never had these problems. Or, this is weird, if it is a mapped domain blog, but there is a site created with the same domain name with no blogs of its own, that seems to work flawlessly.
I just wish I could grasp the whole thing prior to one of my kids, and now my mom, wanting to get active again while their sites are mapped blogs.
Please, if Donncha is watching, could you please explain the difference, and why I had permission problems, and what the heck remote login is?
Thanks.