How I'd do it (sticking only with Generation Three Pokemon and the Gym Leaders for now):
Gym Leaders
Roxanne
"image removed" Relicanth - Level 14
*pokemonelite2000 image removed* Nosepass - Level 16
Reason: Geodude is really overused with first Gym Leaders and it's time for a change. I went with Relicanth, because it would be a nice uncommon Pokemon for people to see to begin with, Torchic users would have a slightly harder time with Double Kick and Aron would be a bit of a pain being part Steel.
Brawly
*pokemonelite2000 image removed* Meditite - Level 19
*pokemonelite2000 image removed* Breloom - Level 23
*pokemonelite2000 image removed* Hariyama - Level 24
Reason: Make Brawly have a more interesting team and start to have evolved Pokemon early on.
Wattson
"image removed" Manectric - Level 27
Reason: Go on, make him the Lt. Surge of the Third Generation. Go on.
Flannery
"image removed" Camerupt - Level 31
*pokemonelite2000 image removed* Torkoal - Level 33
Reason: Two Pokemon that both deserve more attention.
Norman
*pokemonelite2000 image removed* Castform - Level 30
*pokemonelite2000 image removed* Zangoose - Level 32
"image removed" Exploud - Level 33
"image removed" Slaking - Level 35
Reason: Although I was tempted to keep Vigoroth in, I decided against it in favour of something else from a different family. Exploud to be a nice counterpoint for Slaking and Zangoose doesn't get much recognition (one of my favourite Pokemon) and Castform for a bizzare choice, though Spinda also works. I would've loved Kecleon in there too, but oh well.
Winona
"image removed" Swellow - Level 36
"image removed" Pelipper - Level 35
*pokemonelite2000 image removed* Ninjask - Level 36
"image removed" Tropius - Level 37
*pokemonelite2000 image removed* Altaria - Level 38
Reason: I would've loved to keep Skarmory in, but to restrict it to just Third Generation Pokemon, this was the best set with only Ninjask as the new option and a more out there choice.
Liza and Tate
"image removed" Lunatone - Level 42
"image removed" Solrock - Level 42
"image removed" Grumpig - Level 40
*pokemonelite2000 image removed* Claydol - Level 40
Reason: Again, I have no problem with Xatu, but Grumpig needs some love.
Wallace
"image removed" Luvdisc - Level 44
"image removed" Whiscash - Level 45
"image removed" Wailord - Level 47
"image removed" Sharpedo - Level 48
"image removed" Ludicolo - Level 46
*pokemonelite2000 image removed* Milotic - Level 49
Reason: Give him a full team and leave that one seal Pokemon for the Elite Four.
From there on, I would allow Pokemon from other regions to be in the Elite Four team's roster (six Pokemon each), particularly to give more variety to Phoebe and Glacia who desperately need it and the levels starting from Level 50 onwards.
