MU is not necessarily a better choice than multiple installs of standard WP.
If you are looking for a way to control multiple blogs that will be setup almost identically, and/or you want people to be able to create their own blogs on your website, then yes MU is probably a good choice.
If you are managing multiple blogs that have different requirements for setup and functionality, then keeping seperate WP installs may be the better choice.
Here are some of problems I encountered while spending a week playing with WPMU 1.3rc3:
(1) When you do the initial install, you create a main blog in the install directory, and all other blogs added are added as a sub-directory (if you use the subdirectory method) under this directory. This was a minor problem for me, because I could not install WPMU in the root of the domain, so I put it in mydomain.com/info/, which means all the other blogs are a sub-blog of the main one (ex: mydomain.com/info/news, mydomain.com/info/events, etc). This may or may not be an issue for some people.
(2) User registration for all the sub-blogs doesn't work the way I need it to work. When you go to a sub-blog and want to register as a user for that particular blog, it actually forces you to register on the main blog, and then the user has to be manually added to the sub-blog.
(3) If you want to disable user registration on the main blog, then it is disabled for ALL sub-blogs. You can enable user registration on the main blog, and then enable/disable as you like on sub-blogs. This is obviously tied to issue 2 above, but not an acceptable option for everybody.