Less stool output = good. That just means there's less junk filler in the food so there's less garbage for your cat to process. I've noticed this as well.. my resident cat is usually on EVO/Taste of the Wild hard food with a variety of soft foods and his stool are smaller and more firm than when he was on the junk like Iams or Science Diet (eek :) ). My fosters are on Science Diet as well and their poops are always larger.
They will scratch to cover leftovers. If he's not finishing food, just put less out. Unless he is losing weight, I'd not worry that he's eating less food. Again, this can be the result of a better quality food, less filler, means they need to eat less overall.
So I guess I don't see what's happening as problems, per se. But if your cat doesn't like the taste, don't despair. There are other good quality foods that he might like better. The one thing I can say is that some foods are coated in a fat spray to make them more appetizing. It can be hard to transition a kitty that's used to those foods. But try a few options and see which kitty likes best. If you have a smaller pet store or feed store, ask if they have samples of some foods you'd consider purchasing. Canned food.. My cat's all time favorites are Weruva and Soulistic. Soulistic is only available at Petco. Several flavors are shreds in gravy and they're basically meat shreds with a vitamin gravy - super quality. If your cat likes pate forms, check out Authority, Chicken Soup, Felidae. On the other hand, I've had several cats turn up noses at EVO.
I encourage you to stick it out, trying other foods as needed. Sometimes it takes them longer to warm up to new ideas, and sometimes it's a matter of hitting on the right food. But your cat will benefit from your efforts to bring in better quality foods. Good luck!