When I first starting collecting I was the same way, I only wanted complete NES games... I soon realized that if I ever wanted to get an entire U.S. release NES collection , that it was going to be near impossible to do unless I was going to get just the carts. So now I only collect loose carts. When you think about it, what do you boxes and manuals do ? You can't play them, and for about 95% of NES or Atari games they aren't necessary. You can just put the game in and play. If you are collecting for newer systems (N64 , Playstation , Dreamcast) then I would try to collect complete games, but if you are collecting anything older than SNES, I would go for loose carts.
Although , I am the same way about my cartridges. I only want mint games , that look almost perfect. I won't even buy a game if it is less than that.