Iris in Junior Cup and now Ash.
If your going to return character for that many episodes, it to expect he wont be center of attention all the time, and at every moment. When being in cast Dawn sometime took backseat too.
I would definitely replace some of fillers but not all enjoying in Misty or Brock focused episodes, or when older characters like Aya or Duplica returned.The Johto seasons were such a chore that I wish the writers introduced Silver and did the major Giovanni storyline back there. It would have relieved us from those absolutely awful Johto fillers that we could not stand between Goldenrod City and the end of Chuck's Gym. I would have also had Ash meet Ho-oh back then.
I would probably also expand on whole Whirl Cup theme earlier introducing more competitions to develop Misty goal of water master, and there would be more focus on Brock too.
Introduction of Silver would be cool too, and i would definitely do something with GS ball creating one big arc about Celebii in there.
Agreed, i would have him still catch Cyndaquil and Chikorita but Totodile would probably go to Misty's instead. His Johto starters having to fight for screen time with Kanto ones didn't helped things either.And I don't understand why Ash even captured the Johto starters. What purpose did they serve? Either have them do something of value or I'd rather he never caught them at all.
Speaking of direction through which series went i would probably keep Misty in main cast for at least one more region because she wasn't fleshed out enough having more to offer, and had rich personality bringing lot of humor, clash and fresh dynamic which would make cast even more entertaining imo(perhaps joining them for BF to advance her goals). Two girls in cast would be such an interesting concept to try out, but oh well.
Ash would definitely receive rival in Hoenn, being one of main down points imo there lacking someone who would bring tension and force him to push himself forward. And Steven would get more than one lame episode about Aggron.
I would also probably change some of May contest battles which were rather unbelievable and deux ex like whole clash vs Dusclops with Skitty, or against Brock and there would be more focus on some lately introduced rivals like Harley.
In Sinnoh Reggie would probably be Brock rival if i was in charge considering he was breeder too which could lead to some fun development in there. Or Holly, with Brock obsession over girls getting in way of character growing forward. Now that would be interesting to see.
Oh and Ash would probably win Sinnoh league trying to challenge E4 not succeeding in process, forcing him to go on some special training trying to improve his flaws and what didn't worked in BW.