Star Wars Rebellion: I remember millions of Star Wars fans crying about how bad it was. I remember getting it when I was around 11, and thinking it was more of an RTS. I couldn't figure out how to really play it until a year after I bought it. Once I read through the manual and strategy guide, the game proved to be quite fun. Sure, it's a bit limited, especially in tactical simulation where everything is determined more or less by numbers, but otherwise it was and still is loads of fun conquering the galaxy as the Empire or Rebellion.
Star Trek Birth of The Federation: Same as above. The game is actually a lot like Rebellion, except with a more developed research and security ascpet, but minus the characters. Again, people complained about how bad this one was, mostly I think because of the lack of good tactical representation, but I've had loads of fun with it, and still do.