Changes: Get extra PP item before Silph, do not get PP Up
Silph Rival: HD, HD, HD, HD, HD
(Elixir/Ether now) - I don't know whether an Ether here would be faster
Rocket: Acc: HD, HD, IB (Can save one of these Horn Drills and go for a yolo drill on Weezing at low health, since IB is barely any slower)

Get Rare Candy in Mansion and use it.

Erika: EQ, IB, IB
(Elixir now)
Blaine: EQ, EQ, EQ, EQ
Blackbelt: X Acc: HD, HD, HD
(Elixir after Giovanni)
Lorelei: HD, HD, HD, EQ, HD

Champion: X Acc, X Spec: HD, HD, IB, HD, HD, HD

Benefits:
Removes damage ranges on Victreebel, Vileplume, Machokes (Which are 82.9, 97.9, 91.4, & 76.4 respectively (I think))
No sitting through Growlithe Agility
Costs 1 X Sp less. 
Can teach Ice Beam over Rock Slide (and then EQ over Thrash) before Silph to open menu one less time.

Moves are a lot different. Benefits such as Horn Drill instead of RS on Growlithe, but losses such as no Horn Drill on Blaine/Jynx/Rhydon. Idk exactly what time difference would be, but overall probably a decent loss.

Downsides:
Getting Rare Candy and another PP item is slower than getting the PP Up.
Pretty sure you level up at worse times, on the last poke of fights, meaning less redbar skips
I don't think the extra health matters defensively, I think you level out of redbar at Bruno too.