I sure wouldn't reccomend dong this. Reasons include:
1. Many of the parent roms aren't the english version. For example, puck-man is the parent, not pac-man.
2. For 4 player games (which aren't really playable on a two player cab) their 2 player variants are clones of the 4 player parent. So if you want to play the 2 player verison of tmnt, where you can actually select your characters on a 2 playser machine, you are sol.
3. It's going to be impossible to verify your rom set after you've removed the clones. If you are one of these persons that gets their roms all at once (via torrent or whatever) all those clones are going to show up again the next time you get a set.
Just turn off the displaying of clones in your fe, it makes more sense.