Fruit needs to autostack, and honestly flowers should too. But, because of how flower information is stored in the game I don't thinking stackable flowers would be possible with the current system. Maybe if there is a way to stack the flowers for us the user 'visually' but still keep their individual breeding information attached to the given flower once you actually put it on the ground, cool.
Other items should autostack too, like shells, pitfalls, and unidentified fossils. I know the unidentified fossils could cause issues if you try indentify them all at once, but maybe they could circumvent this by letting us give blathers even fossils the museum already has, so let's say I want to id 30 fossils, and have 15 inventory slots. obviously that stack of id'd fossils is too big to keep, but, if blathers says.... "hmm that's a lot of fossils, would you perhaps consider giving them to me to continue my Paleontology research?"and if we say yes, all new fossils will appear in the museum, and all other fossils will go to blathers. Maybe if you donate 500 extra fossils to blathers he'll give you the ability to identify fossils on your own without bringing them to him - since he's seen so many different specimens.
Other than that, give Celeste back her observatory, if the museum store must return, make a gyroid run it haha.
Make rocks removeable, however, when you remove one rock, it will likely show up in another part of town. I think this let's us keep some of the random elements of the game, but I've had badly positioned rocks ruin my ability to place things like bridges, and therefore ruin the flow of the town. In fact, maybe it should be an option to remove the rock itself, but when placing a pwp or house the person placing it will say "oh there's a rock here, we can move it elsewhere, after all pillbugs (or whatever rock bug is in that season) still need somewhere to live too!"
Also, I want to be able to place bushes right next to buildings and rocks. They can surely work out a system of what causes a player to get trapped and what doesn't. Placing a bush right next to a building doesn't cause trapping.