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Gold: 198
78.88%
Silver: 198
78.88%
Crystal: 207
82.47%
Notes
251 Pokemon available in all.
Though the fact that the percentages barely change from Gen I makes it seem otherwise, Gold, Silver, and Crystal actually have a comparatively large amount of absent Pokemon. The absent first gen starters, fossils, and legendaries add up to 18 (Aerodactyl, of course, is obtainable in-game via an in-game trade) while the starters not chosen by the player add six more. Gen II adds a rather weighty six Pokemon to the pool of those which evolve by trade (the most of any generation), leaving ten Pokemon completely inaccessible to solo players. That leaves us with 34 missing Pokemon on top of the version-exclusives.
Like Mew, Celebi is missing in these games, but not in Crystal VC. Of course, in the original cartridge version it is absent. Interestingly, without the VC event Crystal and Silver are identical. When weighing Crystal against other upper versions such as Yellow, Emerald, and Platinum, it's surprising that it didn't add any additional Pokemon - not the Kanto starters, fossils, or even the legendary birds. However, with Celebi included, it still squeaks over the line to be the winner, making this the only generation where all three games have exactly the same amount of Pokemon available (in the original release, at least)!
A very belated edit thanks to something highlighted by
Altissimo: in GS, the player can only get one each of the Fire, Water, Thunder, and Leaf Stones, meaning that only one of their respective stone evolutions is available to the player without interacting with another file.
Fire: Flareon
OR Arcanine (in Gold only)
OR Ninetales (in Silver only)
Water: Cloyster
OR Poliwrath
OR Starmie
OR Vaporeon
Thunder: Raichu
OR Jolteon
Leaf: Vileplume
OR Victreebel
OR Exeggutor
So knock off two for Fire, three for Water, one for Thunder, and two for Leaf for a total of 8. Hey, look at that! Crystal, of course, makes the evolution stones repeatedly obtainable so has no such restriction.
Best value for money:
Crystal (VC)