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Top team is Brendan, bottom is Gold.
Most of this should be self-explanatory but Gliscor is there because Gligar is an Emerald-exclusive in the Safari Zone, and I wasn't really digging Castform. Steven has Metagross and the Hoenn fossils; I didn't want to repeat Pokémon like that. Feraligatr is when Prof. Birch gives you a Johto starter. Since your rival picks what's stronger than you(May, Torchic) I had Brendan pick the weaker one.
Gold was harder. I ended up ignoring the Odd Egg and Sudowoodo so Brendan could have the Battle Frontier Sudowoodo. Gyarados is the Red one, of course. Electrode is from the Rocket Hideout. Umbreon compliments Red's Espeon. Kinda sucks to ignore Tyrogue/the Hitmons, but I just like the idea of the protag catching one of the Electrode when he and Lance split up.