This was asked for in another thread that I can't seem to find in a search for some reason. I agree. The best solution proposed (not by me) was:

Increment "plays" only if you've listened to 3/4 of the song
Increment "skipped" only if you've skipped it before 1/4 of the song has played.

At least I think that's how it went. 1/3 and 2/3 would work as well. Times Skipped isn't currently implemented anyway, but it allegedly will be Real Soon Now.