First, I wish to address the flaws in the gym leaders. They have no purpose besides a TM giver and a checkpoint. However to counter this issue I wish to introduce a new dimension: Victory Road. This would be a new dimension where blocks cannot be placed or broken, essentially a traditional dungeon of sorts full of strong trainers and aggressive high level pokemon cumulating in an Elite 4. Essentially a final goal for when you've caught a few legendaries and have a team of favorite pokemon. A sense of finality before interest in a world fades out. This area would be reached with an item that requires 8 badges to build. The reason why this would be a dimension and not a dungeon is player mentality. In Minecraft, dimensions are new worlds with a higher level of challenge, but more importantly in the End there is only one way out: LOSE. This new stake would give the player a sense of nervousness walking into the final area, which cannot be accomplished by a simple dungeon.
Next I wish to add several features (which are probably planned) these would be Totem pokemon and Dynamax Dens. These would be preferable pokemon bosses, which would challenge the player throughout their journey similar to the role of gym leaders. As I stated earlier bosses need a purpose, which in this case would be give an oppertunity to catch powerful rare pokemon with high IV counts, while simple it is still effective.
Finally, taking a page from SwSh Dynamax battles and Let's Go legendaries. I feel it would be more satisfying when you encounter a legendary you battle a buffed version of the pokemon (similar to ultra necrozma) and when you win you get the chance to try and catch them and if you fail enough times they regain some health and you have to try again. This gives each battle a sense of urgency as the boss is more than a strong pokemon, but a structured fight. Fight-win-catch if fail repeat. This would add more urgency as each ball thrown would be more and more tense as the pokemon will regain consciousness and the battle will resume.