First, read my sig. I am not opposed to using a 2x or 5x experience modifier on Action Replay. Even doubling the rate you gain exp makes the game so much more fun and playable.
Second, I train up matched teams by going through the game again, rather than switching in and out with my already-trained pokemon. Again, Action Replay helps with this because I can reset the trainer battles by holding L and talking to them. (Still looking for a code that resets the gym leaders. If you know of one, PM me.) Anyway, here are the teams I have trained together:
* (current) - Team Eevee - all 7 evolutions plus a normal Eevee. Ironically, the basic Eevee is turning out to be my favorite.
* (next planned one) - Worthwhile bugs - Scyther, Scizor, Pinsir, Heracross, Yanma
Previous teams:
* Humanform - started with Magby/Elekid, added two Smoochums (one ice, one psychic) and a Riolu along the way.
* Tyrogue and Ralts - Hitmonchan, Hitmonlee, Hitmontop, Gallade, and Gardevoir
My starter teams, which include all three starters plus that Gen's basic electric type.
* Red/Blue - Bulbasaur, Charmander, Squirtle, and Pikachu
* Gold/Silver - Chikorita, Cyndaquil, Totodile, and Mareep
* Diamond/Pearl - Turtwig, Chimchar, Piplup, and Shinx
I can't explain why, but training up these teams is way more fun for me than training up individual pokémon. Even now, I can't separate my Magmortar and Electivire. They always come as a matched pair. And I won't use Torterra without its buddies Infernape, Empoleon, and Luxray.