I prune the plants back, and keep the filter intakes both clear and visible. I try not to block the intake at all, because:
1. All of my heating is plumbed through the canister, during the winter months it needs max flow.
2. The job of the filter is to remove crap, so that I can rinse it out of the foam and floss later. It can't do that when there are leaves in the way.
Pruning is a good thing, make it happen.