I wish it was possible to interact more with the different kinds of things you get. It's like most of the stuff you're rewarded with is sort of "empty", like a scooter, what's the point of having that if you can't use it? Or a bike, or a sauna, or whatever. I wish all of the things in the game were more integrated for a more interactive experience, but I recognize that would be one hell of a undertaking.
I also wish the online part of it could be more integrated somehow - for me, personally, I think it would be cooler to live on a larger island with other online players, instead of the villagers, for instance. Would make it more of a "social" thing too, and where you would be encouraged to help one another and co-operate over things. Another one that's not really realistic though.
Also, all the regular complaints - unbreakable tools (the fact that they break are just annoying at this point - it somehow felt more useful to the gameplay in a game like Breath of the Wild), being able to make stuff in bulk.
I sincerely hope there'll be more shops and stuff like that in the future, as it just feels so weird to have this one tiny shop that sells like 4 random crappy items everyday. So much potential to have different shops with different characters. Fruit shop, plant shop, gardening tools shop, gardening furniture shop, indoor shop, bug catching shop, fishing shop etc etc. Those concepts could be so much more expanded upon to make the game more interesting.
I also wish you could just expand somehow, like physically grow your island. Get space for more villagers or people if you do X amount of this, or get so and so many bells or whatever. Feels a bit limited the way it is now.
In general though, I think my biggest wish would be just for the game to be more interactive with all the stuff you get. Decorating and all that is all good fun, but would be a lot more fun if it felt more useful. Like you could play a game of football, for instance, or darts, or you know, stuff like that. Invite villagers to participate in things like that.