This is getting long so I'll post the partial.
Starter: Mudkip (Lyyke)
Route 101: Poochyena (Inky, because I get the feeling I'll be running into these a lot.)
Route 103: Poochyena (Clyde, yup)
Route 102: Wurmple (Lepida)
Route 104: Poochyena (Blinky, JUSTIFIED)
Petalburg Forest: Shroomish (Mel)
Route 116: Abra (Great ball, GO!) Edith. Inky and Blinky both go down at some point in a trainer battle, but who cares? Clyde stands strong.
Rustboro Tunnel: Whismur. I didn't rename this one by accident.
Rustboro Gym: An Oran Berry and two Super Potions give Roxanne's Nosepass a huge HP pool. But I've spent a lot of time leveling Mel, and he's got Absorb, Stun Spore, and Leech Seed. As soon as Nosepass hits the floor, he's Paralyzed. Leech Seed doesn't stick the first time, but the second application starts draining HP. After that it's a matter of not running out of PP for Absorb. Bad luck ruined me the first time around, but it was no contest with Shroomish. Just to rub it in, Mel learned Mega Drain right after Nosepass dropped.
Rustboro Town: May's Wingull fell to Lepida, who has since grown into a Dustox. Mel handles her Treecko.
Granite Cave: Zubat (Obligatory). Stumble through cave in the dark, because seriously, fuck using Flash. Swap out Obligatory for Clyde when I get back to the Pokemon Center. Level up until everyone is in the mid-to-high teens, evolving Edith in the process.
Dewford Gym: I've got a pure Psychic type, a Bug/Poison who knows Psychic and Flying moves, and a Flying/Poison that doesn't have a Flying move yet (when does Zubat get Wing Attack again?) but can whittle things down while taking 1 HP per hit from Fighting attacks. This was a cakewalk. Afterward, Whismur goes into the PC and Clyde comes back out.
Route 110: Electrike (TheShocker). While I vow to put it into storage and never use it because one of the few things I remember about this game is how much Electrike SUCKS, May's Grovyle takes out Obligatory and Edith with Pursuit. Whismur and TheShocker replace them. Grind grind grind up the level difference... >:| Clyde and Whismur both evolve.
Route 117: Marrill (Bob)
Verdanturf: I teach Loudred Rock Smash to get through the tunnel, before the game points out that I can't actually use it until I have another badge.
Mauville Gym: With a Ground-type on my side and Loudred providing backup with a Fighting move against the Steel-types present, this one gave me no problems.
Route 112: Numel (Vesuvius)
Fiery Path: Koffing! (Lyyke KOs with a Tackle crit). Numel! (Lyyke KOs with a Tackle crit). Machop! (Lyyke KOs with a Tackle crit). STOP FUCKING DOING THAT. Machop! Catch it and name it Jann, because I could just get lost in those muscles...
Route 113: Slugma (Hannah). Next fight, Skarmory. FFFFFFFUUUU
Route 114: Swablu (Cuteip).
Meteor Falls: Zubat (LilSlugger).
Mt. Chimney: Maxie's Mightyena takes out LilSlugger.
Jagged Pass: Spoink, given the cautionary name DoNotHug.
Lavaridge Town: I take the Mysterious Egg(tm) as my sixth slot. I swap out the flame-vulnerable Mel for Jann.
Lavaridge Gym: Between infatuation, paralyzation, and general wearing-down of HP over the course of the battle, I switch Lyyke out for Loudred while fighting Flannery's Torkoal. It's immediately oneshotted with Overheat. Jann falls to the same fate, after getting lucky and Overheat missing twice. Torkoal Body Slams Hannah into oblivion. I take out TheShocker and spend his turn using a Paralyze Heal on Lyyke. Torkoal Body Slams and paralyzes TheShocker, but his Static turns around and paralyzes Torkoal right back. Thus emboldened, TheShocker finishes Flannery off with Spark.
Sheesh. With that result, maybe I should have taken the time to level up Bob and used him as a secondary.
With Loudred gone, I need someone else to Smash Rocks. I take Clyde for this purpose.
Mauville City: I bike back and forth to hatch the egg, because I've forgotten what's in it. It's a Wynaut. I name him Boba, so that if he ever evolves he can be WoBobafet. I then unceremoniously dump him into PC storage and get Lepida back out. I spend more time grrrrrinding to even out my party's levels.
Are the names confusing? Right now I have Lyyke the Marshtomp, TheShocker the Manectric, DoNotHug the Spoink, Mel the Breloom, Clyde the Mightyena, and Ledpida the Dustox. Remaining in PC storage are Bob the Marrill, Vesuvius the Numel, Cuteip the Swablu, and Boba the newly-hatched Wynaut.
RIP Inky and Blinky the Poochyenas, Edith the Kadabra, Loudred the Loudred, Obligatory the Zubat and LilSlugger the Golbat, Jann the Machop, and Hannah the Slugma.