The most fun part of speedrunning -- especially Pokemon speedrunning -- is answering the question, "What's the fastest way to beat the game?" Unfortunately, that question has been thoroughly answered for every main Pokemon game. My recent attempts to find alternative, potentially faster routes for Gen 1-3 have been more productive than expected, but in the end I think all the current routes are faster. Here's a breakdown:

RED/BLUE
Current route: Nidoking
Alternative route: Clefable
Why the current route is faster: The manipped Nidoran route is just too perfect. Clefable, although faster in some minor spots, has big problems with Mega Punch accuracy and the Champion fight.

RED/BLUE (CLASSIC)
Current route: Nidoking
Alternative route: Blastoise
Why the current route is faster: It's much more consistent once you get a good Nidoran past Brock. Good Squirtles are slightly faster to reset for, but they rarely can capitalize on Squirtle's theoretically faster early game, since bad encounter or poison luck can ruin an early game.

YELLOW
Current route: Nidoking
Alternative route: Pidgeotto --> Clefable --> Nidoran-M
Why the current route is faster: Although Pidgeotto reaches Mt. Moon very fast, it loses much of its advantage if the Nidoran route manips a Pidgeotto to kill for experience. This manip is similarly difficult to the set of manips required for the alternative route. And Clefable suffers from the same Mega Punch accuracy issues as in Red.

GOLD
Current route: Feraligatr
Alternative routes: Raikou/Entei (possibly with an early Geodude pivot)
Why the current route is faster: Geodude loses too much time to Falkner. Raikou and Entei require a very slow Burned Tower detour, which isn't required like it is in Crystal. I haven't thoroughly timed the legendary dog routes, but they seem much slower for WR attempts, and Pokeguy estimated that the Raikou route is 2 minutes slower after he routed it.

CRYSTAL
Current route: Totodile --> Raikou
Alternative routes: Totodile --> Entei OR Geodude --> Raikou/Entei
Why the current route is faster: Geodude has the same Falkner problem as in Gold. The Entei route can be improved with Hidden Power Electric, but not enough to make up the 30 seconds it loses to Raikou in my original routing comparison.

SAPPHIRE
Current route: Swampert --> Kyogre
Alternative route: Marshtomp --> Tentacruel --> Kyogre
Why the current route is faster: It might not be, since Tentacruel has a much better Tate & Liza fight while also saving time elsewhere. But we haven't found a good enough Tentacool manip yet to justify doing runs, and it's possible one doesn't exist.

(Emerald and FireRed do not appear to have any viable alternative routes.)