1. More Legitimately Rare Pokemon
As of this moment, 649 Pokemon roam five different regions and 17 years of gaming history. Out of all of the obtainable Pokemon, Feebas is arguably the rarest of the bunch. In Pokemon Emerald, Feebas only appears in six fishing spots in an area of roughly 200, and these six spots are randomized. That's right: the ugly little fish is harder to obtain than Kygore and Groudon, the legendary creators of the sea and land respectively, whom are both obtainable in every copy of Pokemon Emerald as part of the narrative.
Gamefreak needs more rare Pokemon like Feebas. As it stands, most Pokemon are captured by scouring the land and seas. Every Pokemon player can capture nearly every Pokemon, including legendaries such as Mewtwo, without much trouble. But not every Pokemon player has the patience or even knows how to catch a Feebas.
Make us jump through some hoops for some of those rarer Pokemon, Gamefreak. Combee can only be captured by spreading honey on specific trees, for instance. More intuitive ways to find Pokemon would open up each region as a place of mystery, and add some much needed excitement and reward to catching 'em all.