You can scale down most rule systems to one or two players plus a GM. Authors have to make assumptions about group sizes; you are by no means obligated to follow them.
In high school I had a long-running Vampire: the Masquerade game with one friend. We both had a ton of characters and switched who was Storyteller back and forth depending on which character was getting the focus that night. It was a lot of fun.
That said, if you're running published adventures, bear in mind the group size they're tuned to and cut the monster numbers down accordingly.
The only system I can think of that definitely *wouldn't* work for a group of two is Paranoia, and that would probably be fixable with sufficient worldbuilding. (But you may as well play GURPs at that point.)