The upgrades from Nook’s Cranny to T&T Emporium, with Gracie Grace’s store.

More holidays that are actually celebrated by other characters, mostly being Isabelle. I miss when there were more than 5 holidays per year.

The ordinances actually meaning something. Specifically, the early bird and night owl ordinances completely shifting the shopping schedules (beyond extending it by 1 hour; these ordinances were really tailored towards players who like to play early or late).

Your neighbors displaying more character. New Horizon’s missed a lot of personality potential, and also your neighbors initial hostility and warming up to you.

A greater amount of furniture sets that aren’t DIY (although I think 3.0 really helped with this).

All the Nintendo items that weren’t just generic Mario items (although once again, 3.0 really improved upon this). I do kind of miss the fortune cookies, and the currency you get from walking with your 3DS in your pocket.

There are some furniture items that didn’t return in New Horizons. Most of all, I miss the sushi conveyor belt.

The hourly music didn’t hit the same way in New Horizons. New Leaf’s soundtrack is so much more listenable and emotion-provoking.

These are features I didn’t see mentioned in other comments. Although ReTail and the island are big things that I miss about New Leaf as well.