The biggest gripe for me (and one that was probably never going to be remedied in the first place) is the fact that terraforming and redesigning your island's layout, despite arguably being the game's biggest selling point, is a very tedious process that hasn't been improved upon at all over the last year. The fact that making adjustments has to be done square by square, and piece by piece, is nightmarish for somebody who wants to make significant changes. Throw in the fact that moving structures can still only be done once-per-day, and still requires having the space you want the building to occupy be vacant, and it makes it really hard to appreciate that they (still blessedly) reduced the cost of doing so drastically. I was very excited when they incorporated Happy Home's decoration interface into New Leaf and carried it over into New Horizons, but it makes not having something similar for decorating your island that much more egregious to me.
Ideally, there should have been a system right from the start that would let you design the island from an overhead view and would let you draw terrain, cliffs, water, paths, etc. and drag and drop buildings and structures where you wanted them. You could pull items from your inventory just like with the housing interface and place those wherever you liked as well. Then, in keeping with Animal Crossing's "play every day" motif, they could have simply rolled all of your costs for the adjustments together into one lump sum (or perhaps even a new loan if you'd already paid your house off) and then had the new layout take effect on the next calendar day. It would have been a great way of making the process of redesigning your island much more efficient and enjoyable, which would have given me a greater reason to keep coming back, since shaping my island was very much the most interesting thing in New Horizons for me that wasn't present in previous games (save for New Leaf's relatively limited take on it).
The thing is, if it's not something that had been planned at some stage during development, it would probably be a nightmare to try and incorporate now. I don't want to chalk the current system up to simply wanting more padding, but from my perspective at least, something like this seems a no-brainer. It all gives me the feeling that they may have wanted to give us something like that from the get-go but it would have required more development time than they could afford. Fingers crossed that they slip it in at some point, but I'm mostly resigned to the idea that it'll just be among the big features in the next game.
As for everything else, it all pretty much just comes down to QoL. Most of y'all have already mentioned that the multiplayer element still needs a ton of work, both in regards to the tedium of the process and the general lack of activities to partake in. Just to tie that into my previous remarks, giving Best Friends the ability to design your houses and islands with you would have been enormous, not just for the sake of fun but for the sake of making the current system much more bearable. But I'd imagine that would be even more of a nightmare to implement, given the technical limitations, so I'll just keep dreaming about it for now.
EDIT: As one added note - All the talk about the megaphones reminded me of one of the biggest things that's puzzled me since day one. You have a phone and presumably everybody else on your island does as well. Why can you not simply call a villager to locate them or invite them to do something or literally anything else? Sometimes it feels like somebody on the development team forgot you can use your phone for more than Amazon or emergency services.