A difficulty system is planned by the developer!
About Skills: Some of the skills make some feedism upgrades redundant.
Some of the feedism upgrades where already replaced by skills, but basically everything that has to do with numbers, like how many calories meals have, could be skills only. Unlocking features should remian feedism upgrades.
You're right, the levelling system is due a revamp (it's not that different from how it was in the original version of the game, but a lot has changed since). I'd love to add skill trees and make levelling feel more like a journey. Imagine Feeder, Feedee and Fitness skill trees, with, say, 50 levels, and lots of decisions as to which upgrades to pick.