To start with, there's the language they're written in. My experiences with Git and Mercurial have been very similar, but I know that if I want to tweak Mercurial, I can do it, because it's written in Python. Git is at least somewhat in C, which I'm not as familiar with.
Git and Mercurial are what's called distributed. Every copy is created equal, and they can push and pull (using that terminology) changes from each other on an ad-hoc basis. Subversion, on the other hand, consists of a single central repository, and each working copy is a slave to that central server, pushing and pulling (committing and updating, in this case) changes from it and it alone.
Installing Git or Mercurial for a couple of people consists of getting SSH access to the same server and installing a couple of packages. Whereas for SVN, as far as I know you need to configure and run an actual server application under Apache, and then mess with an SSL cert and .htaccess, etc. to secure it.
For all my personal projects, I go with Mercurial or Git. If I were working with a large team, I'd probably go Subversion because you get centralized authentication and hosting. But for two people, I'd pick one of the distributed ones, because then you don't have to mess with centralized authentication and hosting. :-)