I'm working on an engine right now, and one of the things I was considering doing in the future was using it to make a class-based CTF game, which is, let's say, inspired by the Team Fortress games, specifically the first one. None of the assets or code are the same or similar—it uses assets from a different game on the same engine and I don't have the source code to either game, and it's third person, but can the classes themselves being essentially straight from Team Fortress get me in any legal trouble?

You can go out of your way to make your character concepts and assets very different from their Team Fortress counterparts, making it obvious that you are making a similar game in the same genre, not violating copyright or even trademarks.

What are the obstacles to designing a CTF game with different and improved rules and/or a different setting? It would be easy and fun.