Gen 3's box management is a godsend, especially when transfering to Bank requires you to put everything in Box 1 in RBY/GSC and it takes forever to move everything around in those games. I also like how the later games give you unlimited bag space, I hate having to constant deposit items in your PC.
Honestly I couldn't give a shit about the older games lacking things like a physical/special split or abilities. The games are easy enough that you can beat them with shit movepools and it's nice not having to worry about Poison Point/Static/Sturdy/etc. And then you have things like Thunderpunch Typhlosion and Sceptile actually being able to use its signature move effectively.