Ok, so you know how in the beginning, after you deliver the package to Prof Oak from the Pokemart, you can battle Gary (or whatever you named him) on the path to the Pokeleague? Well, up until that point in the game the only Pokemon you can catch are Nidoran (male and female), Rattata, Pidgey, and Spearow.
If you chose Squirtle, then Gary chose Bulbasaur, a plant Pokemon. Both bird and poison Pokemon are effective against grass Pokemon, so you can use your newly caught bird/poison Pokemon against Gary’s Bulbasaur with great success.
Further, in the beginning of the game it is the hardest to beat other Pokemon, both because of your low level and the limited types of Pokemon you can catch. So any advantage at the beginning of the game is better than any advantage at the end of the game.
Also, the final gym leader uses rock Pokemon, which are weak against water Pokemon.
And that is why Squirtle is the best.