I'm honestly not even mad about losing the skills in the update. I see where the dev is coming from where it will cause balance issues while incorporating timers in the late game when you have all these maxed out skills. So far, the familiarity system they incorporated instead has been great. I do feel like breaking doors should kinda be a true to each other type of thing (each door broken in a loop will make it easier to break all doors in every loop. I understand it probably will never be like that because it would be a pain in the backside to code into the game.
So far it seems nice. I just wish there was some indication as to when certain things unlock (new creatures to control, the ability to finally move around to unlock fruits was a nice surprise when I finally unlocked it). Just little QoL implementations that give the player a sense of the "next goal" is what I mean.