Yeah I've always thought about this, here's what I would have liked to seen the gym leaders have:
Noctowl (12), Skarmory (13)
Basically leave the Pidgeys/Pidgeotto/Spearow/Fearows to the gym trainers, and emphasise Johto's birds. Skarmory might be too harsh for Chikorita fans, but I'd make Mareep and Wooper available earlier to help out.
Ledian (16), Scyther (18), Pinsir (18)
Once again the Butterfree & Beedrill families can be relegated to the gym trainers, and we give the undervalued Pinsir a spotlight to shine.
Clefable (21), Miltank (24)
Whitney's team is fine, I've evolved the Clefairy for extra bulk, and some level boostage too. More needs to happen between Azalea and Goldenrod, like maybe actually having trainers in Ilex forest.
I've always thought Morty should have just the 1 Pokemon but make him almost impossible to beat (like Lt Surge in Yellow version.. that Raichu with Mega Kick,
), with a really amazing moveset too.
Primeape (32), Hitmontop (32), Poliwrath (34)
Yeah yeah I know that Hitmontop should be "reserved" for Bruno's team really... but since Bruno leads with Hitmontop anyway I don't think the Top is really Bruno's signature Pokemon. But Chuck's team definitely needs more Mach Punch and more Close Combat.
Magenton (35), Steelix (38), Ampharos (38)
Agree with this. Was going to replace Ampharos with Scizor but Amphy is fine too.
Dewgong (38), Jynx (40), Piloswine (41), Lapras (42)
Agree with this too. I don't know, ice Pokemon kinda suck offensively... I'd probably make this the 5th gym (after Morty before Chuck). Agree hard with Lapras though, not really sure why he's not on Pryce's team in the first place.
Gyarados (45), Dragonair (46), Kingdra (49)
Once again agree.
Girafarig, Xatu, Slowking, Exeggcutor, Espeon
(Can't be bothered doing levels)
I think Will/every 1st Elite should have a very diverse team with secondary types... My selections are based more on Johto dex possibilities.
Muk, Nidoqueen, Tentacruel, Crobat, Ariados/Foretress
Wow I love your Nidoqueen and Tentacruel, and I think Koga's team at the moment is pretty perfect already, so I've bumped off Venomoth, and can't decide which one to keep out of Ariados and Foretress because they are both junk ingame, but are very "koga" so I don't know which one to bump.
Hitmonchan, Hitmonlee, Steelix, Heracross, Machamp
I don't really know about Steelix, was considering Marowak instead but I guess he works. Heracross needs to be in there as he's a staple Johto Pokemon but I always forget about im because you can only catch him headbutting trees!
Umbreon, Murkrow, Houndoom, Vileplume, Tyranitar
I've put in Vileplume instead of the extra Houndoom just for variety.. but yeah Tyranitar for sure.
Gyarados, Aerodactyl, Charizard, Dragonite, Dragonite, Dragonite
Same goes. I found Outrage Dragonite hard enough to beat so I don't have a problem with this team.
A lot of my justifications are because I don't think the gyms "highlight" much of the Johto Pokemon fairly, whereas with the new games all the Gym leaders are given new signature Pokemon that are available in the dex, which emphasises the strengths of those new Pokemon introduced. It's a bit sad how Heracross is almost forgotten about because you don't bump into him at all, or Tyranitar and his family are largely ignored, so if i were to be doing gyms again its not because i want a better challenge, its for the reason above.