>>22274868An actual endgame, actual challenge with dungeons going up 99 floors into legendaries and even better, dungeons which clear your items, reset you to level 5, and go up 100 floors with a legendary boss waiting for you at the end which is going to be so fucking satisfying to recruit.
More involved plot with slightly more developed characters (in Explorers of the Sky at least, I never thought I'd care about fucking bidoof, sunflora and wigglytuff of all Pokemon)
Then all the Pokemon, a more personal connection since you get your starter based on a personality quiz, you get sidequests and you had things like IQ to build up your Pokemon to its top potential, while what Pokemon you used actually mattered.
Also in the older games I thought the smallest thing was the tightest shit, but you could steal from the kekleon shop and when they went after you, you could fight them off and even recruit some.