Nice ideas for the gyms, I'd do something similar. I'd definitely keep all the same signature Pokemon though (save for new evolutions), and also, I'd throw in a few Gen 3/4 pokemon too. One of the things that annoyed me about FR/LG was how it was too much of a straight remake, only allowing you to catch Kanto pokemon (bar the Sevii islands). We've got new pokemon, we may as well use them. I know some people don't want any changes from the original, but I'd much prefer drastic changes to playing the same game again with updated graphics.
Falkner:
Spearow (lvl. 10)
Hoothoot (lvl. 10)
Pideotto (lvl. 12)
Maybe he should be a little stronger, but that team feels good. The levels needed upping, Spearow is stronger than Pidgey, and Hoothoot gives the team a Johto element.
Bugsy:
Ledyba (lvl. 13)
Spinarak (lvl. 13)
Beedrill (HG) or Butterfree (SS) (lvl. 14)
Scyther (lvl. 17)
I've always liked the idea of gym leaders having different pokemon depending on which version you're playing, so I've done that here. Ledyba and Spinarak replace the useless cocoon pokemon, and Beedrill/Butterfree add a little extra to the team. Scyther is tough enough as he was in the originals, so I've only given him one extra level.
Whitney:
Clefairy (lvl. 18)
Glameow (lvl. 17)
Miltank (lvl. 21)
Whitney's team was decent enough in the originals, but a little small. Clefairy's the same, and I've just added one level onto Miltank, as she was a real bitca to take down. I've thrown in Glameow because it pads out the team and fits her theme of "cute" pokemon.
Morty:
Sableye (lvl. 22)
Haunter (lvl. 24)
Misdreavous (lvl. 26)
Gengar (lvl. 28)
Morty was always a bit of a shady character, so I've given him a dark-type in Sableye, who's always interesting to battle, what with having no weaknesses and all. Misdreavous adds a Johto element and keeps the team from being too focused on the original Ghost trio from Kanto. I've added a few levels onto Gengar, and he'd have a better moveset too, as he was surprisingly easy to defeat in the originals.
Chuck:
Primeape (lvl. 31)
Machoke (lvl. 32)
Hitmontop (lvl. 29)
Poliwrath (lvl. 35)
Chuck in the originals was, frankly, a joke. The fifth gym leader needs to have much more than two pokemon. Hitmontop gives that all-important Johto element, and no fighting team in complete without a Mach-mon. The levels have also been upped significantly.
Jasmine:
Magneton (lvl. 36)
Skarmory (lvl. 34)
Lanturn (lvl. 37)
Steelix (lvl. 38)
Steelix was a good pokemon in the originals, but a little low-levelled, so I've upped them. However, her support pokemon were ridiculous (two Magnemite?), so I've evolved Magnemite and given her Skarmory to cover her Ground weakness, and Lanturn to cover fire. I know Lanturn's not a steel-type, but it's not uncommon for gym leaders to have one or two pokemon outside their speciality, and Olivine is a seaside town, so a fishy pokemon looks right on her team.
Pryce:
Dewgong (lv. 39)
Piloswine (lvl. 40)
Sneasel (lvl. 40)
Mamoswine (lvl. 42)
I've evolved his Piloswine, but gave him another and kept Dewgong, though the levels have been upped. Sneasel is a good pokemon that adds another typing to his team.
Clair:
Seadra (lvl. 41)
Dragonair (lvl. 41)
Gyrados (lvl. 42)
Dragonair (lvl. 41)
Kingdra (lvl. 45)
Clair was just about tough enough in the originals, but I wanted to get her levels a bit higher so I could drastically up the Elite Four's levels. Three Dragonairs made her a little dull to battle, so I've taken one away and given her Seadra and Gyrados to make things more interesting.
I'd change the Elite Four more drastically. All of them should have full teams, as they are the four most powerful trainers in Kanto and Johto, it's silly for them to have an empty slot in their party. Also, I'd give them more noticeable signature pokemon (because does anyone remember Wills or Kogas?), and up the levels significantly.
Will:
Xatu (lvl. 46)
Slowking (lvl. 42)
Gallade (lvl. 47)
Solrock (HG) or Lunatone (SS) (lvl. 45)
Jynx (lvl. 47)
Alakazam (lvl. 50)
Alakazam is THE psychic pokemon, I was shocked that neither him nor even Kadabra was in Will's original team. He is now Will's signature pokemon, and a whole 8 levels higher than his previous highest level member. I've added the Lunatone/Solrock for more version differences and a good typing, as well as Gallade to combat Dark-types. Slowbro is changed to Slowking, who has higher Special scores, and will be given a water-type move, which he lacked originally. Xatu and Jynx keep their places, but their levels are higher.
Koga:
Weezing (lvl. 46)
Ninjask (lvl. 45)
Venomoth (lvl. 48)
Nidoking (HG) or Nidoqueen (SS) (lvl. 48)
Crobat (lvl. 50)
Scizor (lvl. 52)
Koga's team was difficult to decide on, and ended up quite different to the original. Venomoth and Crobat were kept, but Forrestress was booted in favour of Ninjask, who fits Koga's ninja theme much better. Muk was replaced with Weezing, who gets immunity to Ground (making ½ the team immune to Ground), and the Nidos were added, adding a lot of versatility to the team (they can both learn moves of all types bar Grass). I had trouble deciding on a signature pokemon. Crobat sort of filled this role in the originals, but was too weak to be memorable. I toyed with the idea of Drapion, as he has a psychic immunity, but he was already a signature pokemon in the Sinnoh E4, so I went with Scizor instead, who fits the whole ninja theme well.
Bruno:
Hitmonlee (lvl. 48)
Steelix (lvl. 51)
Hitmonchan (lvl. 48)
Rhydon (lvl. 50)
Lucario (lvl. 52)
Machamp (lvl. 54)
Machamp is once again Bruno's signature pokemon, and the Hitmons find their way back onto his team, though Hitmontop is excluded as he has already been on Chuck's team. His trademark Onix has been upgraded into a Steelix, and Rhydon and Lucario have been added for extra type differentiation (and for being damn cool).
Karen:
Umbreon (lvl. 53)
Gengar (lvl. 53)
Honchkrow (lvl. 51)
Spiritomb (lvl. 53)
Weavile (lvl. 54)
Houndoom (lvl. 56)
This team hasn't changed drastically, but gone is the not-dark-type Vileplume, and her Murkrow has evolved. Gengar, Umbreon and Houndoom stay as they are (though if I were making this game then the Pokedex would contain my own made-up evolutions, so Murkrow would have evolved into Vulkrow, and Houndoom into Cereburn). Spiritomb, also being Ghost-type, fits the theme, and Weavile is an excellent pokemon that adds another typing.
Champion Lance:
Charizard (lvl. 55)
Dragonite (lvl. 58)
Salamence (lvl. 58)
Aerodactyl (lvl. 55)
Kingdra (lvl. 56)
Dragonite (lvl. 60)
Lance loses one of his legendary Dragonites, but gets a Salamence to make up for it. Charizard and Aerodactyl also make return appearances, but Gyrados is replaced with Kingdra for resistances against pretty much everything. Also, it is the only Gen II Dragon-type, or even quasi-Dragon type.
So yeah, that's pretty much it. What do you guys think?