These are great ideas. Some are actually coming in the next update.
With nature, there's a few different types, some which can be stored, others which cant. "Tendables" like flowers, can be stored, because they aren't removed from the game. Rocks and trees and grass are intended to not be stored, because expansions would be a bit too easy to clear when you unlock them
XP from collecting crafting is a great idea, and something that should have been in.. I'll follow up tomorrow (in a few hours actually) and make sure that we have that in place for when we update the server.
There will be a way to earn gems, but not until you have a certain building that you unlock at level 10