I would recommend checking out Mutants & Masterminds. It is not my favorite superhero RPG setting, but it is easy to learn, and you can do just about anything you want to with it. It uses a simple d20 mechanic, so that won't be much of a departure from 3.5 for you. Since you only plan on having one DM and one player, you won't really have to worry about balancing the characters out so everyone can have fun and not just one superhero knocks out all the bad guys. Like I said, there are other superhero systems out there that I prefer, but this is a good one for starting out.