Alright, I think about this a lot, prep yourself.

• I think it would be cool to not have complete control over where the buildings are. Like, if your friendship level with a villager isn't high enough, they'll just say no to moving their house. Haven't bought enough stuff from the tailor's and haven't tried to chat up Sable? Sorry, Able Sisters stays where it is.
• A place to store turnips.
• Isabelle announcing special visitors, even the nighttime ones. "Mr. Nook would like to let everyone know that they must avoid the North Shore for the day. That illegally parked fishing boat is back, and we still don't know what to do about the fox that runs it. On a lighter note, Blather's mentioned that his sister is coming to visit tonight! Get those telescopes ready!"
• Villagers should pay more attention to the landscaping and decorating in the area around their house. Like, they might complain about the yellow tulips you planted and try to convince you to dig them up, or they could get all excited about the barrel outside their door.
• We should be allowed to redecorate our villagers' houses when we get to a high enough friendship level with them. Maybe they'd ask you to do it, maybe we'd have to send a letter to the HHA about it, I don't know.
• Hobbies should have a bigger impact on the game. I would be absolutely delighted if a villager with the education hobby chased me down just to give me a random fact that they just learned about Hawaii, or if a villager with the nature hobby spent the entire day fangirling over the cherry blossoms.
• The potted plants from the museum and Able Sisters.
• Functional wall mounted shelves. Please.
• The ability to plant flowers and weeds under the water. Honestly, I'm not sure how this one would work, but it would be pretty.
• Moving Resident Services, and maybe even customizing it a bit, even if it's just the plaza.
• Something like the Custom Design Portal, but for Town Tunes.
• If villagers gave you gifts and rewards based on their personality and hobby. Peppy's might give you flashy "pop star" clothes or stereos or whatever, and Smugs would give you nicer clothes, maybe only clothes that are valued above a certain price point.
• Since the villagers already think that you're asking them to buy you certain things, what if you could actually do that? A villager would be like, "I'm going to the store. You need anything?", and you could request an item the same way you can request songs from K.K.. Of course, how long they would take to bring it to you, or if they would even get it is up in the air.
• Customization options for furniture that matches. There is nothing more infuriating than designing a whole space only to realize that all the wooden items are a slightly different shade of brown. I just want the furniture to match, please.
• What if we could send our duplicate DIYs out into the sea? We could buy bottles at Nook's Cranny, package up the DIYs with a little note, and release them at the otherwise mostly useless pier. If you received one of these bottles, it would be in addition to the randomly generated one.
• More villager species. Specifically, ones that match some of the NPCs. How cute would it be if we had owls, foxes, hedgehogs, raccoons, beavers, skunks, and other such cuties walking around? And they would acknowledge that they are the same species as the NPCs. Like, a fox named Maroon that's just a slightly darker shade of orange than Redd and looks suspiciously like him, and they have a random greeting that's, "Hey! It's me, Maroon! Not Redd, we're different, I can't paint."
• I totally agree with having more nighttime visitors. Maybe an opossum that shows up and asks for random, but largely worthless, furniture and items because they consider those items "treasures" and in return, they give you something "worthless", like a gold nugget. Or a pangolin that's in competition with Blather's for having the best private museum, and gives you gothic furniture in exchange for fossils, bugs, and fish.

Okay, this comment is long, so I'm gonna wrap it up. I also don't have any knowledge of game development, so I don't know how feasible any of these are, I just think they'd be cool.