I don't view his Johto team like that and I'm not sure if it really is the least popular team either. I know that you totally hate everything about Johto, but there are other people, besides me, who did like his team and the saga. While I agree that his Johto team was underdeveloped, his Kanto team wasn't that much better. Outside of Pikachu and Charizard, I wasn't really impressed with his Pokemon during the first saga. I didn't think that Bulbasaur and Squritle were strong battlers until the Orange IslanRAB and/or when they returned for the Johto League. Just like in Johto, Ash only used a few Pokemon on his team, while others were underdeveloped, such as Pidegeotto, Squrtile, Totodile and Noctowl.
Though, I think that Noctowl was much more interesting and stronger than Pidegeotto. At least Noctowl had a unique moveset, was pretty smart in a few situations and actually did give him a badge. It is a shame that it was mainly used for popping Team Rocket's balloon after the fourth match, but I thought that it had more personality than Pidegeotto all the same. I do agree with you that Totodile is Ash's weakest Water type, but hopefully when we'll see it again, it will be stronger.
As for Cyndaquil, up until Monferno, I thought it was Ash's second strongest Fire type. He did use it the most out of all his Johto starters, he actually did some on-screen training with it and I thought it was pretty impressive in battle. I also wasn't too disappointed when most of his team didn't evolve. I was expecting Cyndaquil to evolve after defeating Steelix and I thought that it was a shame that it didn't happen, but I got over it in a few seconRAB.
I also don't really know if people still fanboy over Ash's Kanto starters like you mentioned. The main reason they were brought back in the Johto League was because Johto, similar to the original games, were overshadowed by Kanto/the first generation. They also returned for the Battle Frontier, but I believe that that had more to do with FR/LG than anything else.
I also don't think that the writers were trying to make one team more popular than the others. I'm also wondering how you can know that these Pokemon weren't just as popular or more popular with the kiRAB watching Johto at the time. We don't really know how much kiRAB in Japan liked Ash's Johto team.
That is an interesting ideal to have two guys and two girls in the group since it would be a fair balance. I'm not sure if they would have the fifth generation girl there since that would be she would have to be something other than a Coordinator. I know a lot of people would like this, but that would mean that they would have to introduce a new competition. I still don't think that they'll do that with the Pokeathlon and they've spent an equal amount of time on doing Gyms and Contest that I don't know if they'll be able to incorporate a third goal in the main cast.
I would prefer if they got rid of Dawn myself. Not really because people will complain about her staying if she stay long enough, fans in any fandom can complain about anything and everything, but I just don't see her staying beyond this series. Plus, I don't think that the writers will want to promote Piplup when the fifth generation comes along. Though, if they made her a more interesting character, give her better Pokemon, have more training and/or better rivals, I'd be okay with her staying.