I usually edit the aircraft.cfg and remove any schemes there that I will never fly.
If it's one I want to remove temporarily, but still have it available for FSX to use as AI for example, edit the "panel=" line to read something like "panel=none"
If FSX can't find a panel, it thinks it's just for AI & won't list it in the selection screen.
Or you can just change the options to not show all variations.
Then you get only one example of each aircraft.
Problem is, you can't choose which example.
You don't even have to type =None Paul.. =n will do. Works for idle gits with thousands of paints like me
As Dave says.. if space is an issue and there are paints you're NEVER going to fly, it's probably as well to remove the paints completely (or to disc) along with an original copy of the aircraft.cfg then edit the cfg to remove those paints by taking out the associated [fltsim.x] sections then renumbering what's left.. not forgetting that 0 (zero) is the first number in sequence Beware though.. don't delete unnumbered texture files or ones any of your other paints alias to in the texture.cfg's of your remaining paints