They don't have to sacrifice the story mode for the battle system or training. They choose not to make it better.>>54257
Crystal Clear is probably the best one I've ever played. It's open-world and you can start in any town if I remember right. There are new trainers (self-inserts of the devs), new areas, tons of new music (Lt. Surge has Guile's Theme and the starting map screen where you pick a hometown has Pokemon TCG map music, for a couple examples), some easter eggs/events/secrets, trainers scale with your badge count, you can customize your sprite/pallette, quality of life improvements, etc. all while maintaining compatibility with Stadium and the vanilla roms.
The Drayano hacks that make all Pokemon catchable and improves all the trainer battles are good, too.
Prism was another interesting one. Has a couple new types and you get Larvitar as a starter.
FireRed Backwards is cool, too. They changed the overworld a ton and you do leaders in a different order. The starters are kabuto, hoothoot and machop I think. Haven't played it in awhile and always chose kabuto.
I think someone rigged together a story mode for the Spaceworld Gold demo that got leaked, so that could be fun playing with the cut roster.