Hmm, that's a good question. Stat-wise, the only possible benefit would be the slightly higher Speed of Magneton, but considering that it's not meant to specialize in Speed (and that its other stats improve upon evolution to Magnezone), the Speed change is inconsequential. The only oddity I noticed, in checking a GameFAQs guide, is that Magnezone doesn't have any Egg moves. This could just be due to an error on the part of its creator, or it could mean that people interested in breeding for something like Night Slash may want to keep their Magnetons unevolved.
As I'm sure you're already aware, there is a benefit in keeping Magnemite itself unevolved, as it learns many moves earlier. If it's already become a Magneton, though, it's a little harder to find a reason to prevent its advancement. Very curious....