This is a judgment call that depends on the situation. When you're trying to maintain trails, our advice is to always look for a natural cure first. For example, we've seen leaves temporarily help to fill in naturally sandy areas and make them more stable. Also, when leaves cover a trail, no matter how well you know it, it changes your perspective and will make you wonder,"Now where was that rock?" And that can keep speeds down and make the trail friendlier for all users.
For beginning riders, however, leaves obscuring obstacles can prove problematic. So we usually recommend removing leaves from loops used by less experienced bikers.
Also, you might think that leaves help to eliminate or reduce mud and erosion damage. But, they're really not much of a help. If there's a mud hole, even a small one, letting it fill up with leaves will add to the problem by holding in the moisture and preventing the hole from drying out which, as you know, makes the mud hole grow and become bigger, deeper and meaner.
Mud is mud and should be removed from the trail. Then the trail bed in that area should be re-contoured to provide adequate drainage to prevent water from ever sitting on, or running down, the trail again.
Summing up, we're usually in favor of leaving trails natural (leaves, rocks, some trees), but there are exceptions and we recommend carefully considering the consequences before taking action.
For more great trail tips and information visit IMBA.