One could adjust point totals for the game to account for the fact that the PC will generally be out numbered, grant advantages that account for the fact that they'll be outdone as far as action economy goes, and the game itself has no particular expectation of playstyle so there's no requirement for a team to be present.
For what it's worth, I don't even particularly like GURPS, but generic systems tend to be easily modified to suit a duet game; since unlike options like D&D, they by their nature aren't typically designed expressly for team play.
I've done many duet games, the big thing one needs to be concerned with is the action economy. There are a few ways to get around this. You can make it so player's in combat actions amount to more (Crawford's solo rules for Labyrinth Lord, Stars Without Number, and Scarlet Heroes does this), you can give the PC more actions, you can implement supporting NPCs, or you you can have enemies act less (this is the default solution for action movies and video games). Personally I prefer to run the game as is and just accept that the PC wont be able to take on as much all at once, this encourages stealthy approaches and works best in systems with minimal HP mechanics (since a damage sponge enemy basically necessitates standing there and duking it out to deal with).