like maybe some sub category's i don't know i just know that there is too much in that folder, just saying

471801 maybe get rid of the ones that have the most dislikes

Perhaps you should go through, find which ships are the most popular that aren't listed and create a folder for them and for those that aren't as...common or popular, leave the Others folder for those?

513190
Pretty good idea here. Maybe add like a TaviScratch or something? It feels like some Other ships are more common than some of the Mane 6 ones.

I think the solution is relatively simple.
Yeah, a few common pairings from the background ponies might help. Scratchtavia. LyraBon.

But I think the real difference would be made by just putting in maybe five new folders for the very common 'targets'.
Celestia, Luna, Big Mac, Wonderbolts, Spike.
Probably.

Then again, most of those probably have their own groups. Which is probably why you won't see much change.

At this point putting something into Shipping>Other is pretty much the identifier that YES, you wrote a shippy fic containing a non-Mane-6 pairing.

I think folders for anypony/Main Characters That Get Shipped is a good idea. Like Luminary suggested. An anypony/Celestia folder or anypony/Spike folder, etc.