ROM Hacks that genuinely improve the base game?

[Masterofthefalcon]

Shadow the Hedgehog: Reloaded takes a pretty lackluster game and cranks it up to a solid 7/10. Fixes a lot of the control issues in the original and fixes the mission structure, along with other small QOL fixes that really help this game out. Keep in mind though, the hack isn't as extensive as something like Project '06.
My playthrough was enjoyable and kind of made me wish Sonic Team had more time with the development of it.

 

[R66-Y]

My personal favorite is the ALTTP Randomizer (i dont know if it counts?) improves the base game a lot in terms of replayability plus better menus speed, faster text boxes, and even you can customize the player sprites in the setup of every run/seed
I can play A Link to the Past with this hack over and over again and it always feels fresh because of the randomness of the item placement and the challenge that comes with it.
It's amazing.

 

[Bakuma1997]

One that makes a simple change, but one that makes a big difference

¿Ree that in DQ IV the Playstation remake lets you talk to your party members? the coding wasn't removed from the DS version, but oodly enough it wasn't IMPLEMENTED, the Party Chat patch allows you to talk to your party members again, the big difference is the fact that i feel the Chosen suddenly turn into statues that follow your orders as soon as you reach Chapter 5, a shame since you spend the first four episode seeing their characterization

And yes i am aware of the Mobile versions restoring it, but i don't like playing DDR in my touchscreen while i have buttons aviable