I think the best version combination would be Yellow, Gold/Silver, and Crystal.
http://bulbapedia.bulbagarden.net/wiki/Game-exclusive_Pok%C3%A9mon
As shown in these charts, all Pokemon that are not in Yellow are in all Gen 2 games, while Vulpix(in case you choose GC) and Mankey(in case you choose SC) can be found in Yellow.
A key difference in Crystal is that Sneasel is found at the Ice Path instead of at Mt. Silver, and Larvitar can be purchased at Celadon Game Corner with 8888C. This Larvitar is at Lv40, which is much higher than the level of any wild Larvitar you can find at Mt.Silver.
However, Misdreavus is only available at Mt. Silver in all Gen 2 games, thus it is the bottleneck of the run, just like Mewtwo in MrWint's R/B 150 TAS. The best plan is probably to have either G or S rushing to Mt. Silver by getting all Kanto Badges and C collecting legendaries(since you have to revive three beasts any way) and getting coins in Celadon Game Corner for Larvitar. It might be a good idea to use the Yellow rom from 3DS VC so you can play the surfing minigame in case there is much free time.
It seems the notes on ISM's run from 2012 mentioned N4 green, which is the only new skip featured in current RTA WR. Could anyone please help translate this text? The time spent for S3 green in vlackSR's WR is longer than the time spent for both N4 green and S3 green combined in ISM's run, but I'm sure the time spent to skip N4 green can be more optimized in a TAS.
Don't know if anyone has tried fat Wario clipping at the left wall of the very first room in N1. I wonder if there is any chance to get into the black area below the boss fight room and teleport into the tree. If Rudy's hand is considered a heavy enemy, the only chest can be skip is E3 green even if N1 blue early is possible.