I always pick the Firestarter, dunno why, maybe just beacuse I love 'em. Yeah, if you pick Charmander, it'll be tough the first two gyms, but it's a real pain to find good fire-pokes in Kanto, and even due to it's poor movepool, Charizard is a good pokemon ingame, so go with the one you like most. Remember, it'll be hard with Firetypes the first two gyms, and easy with the Bulba, but just try and choose. And think about the legendary dogs, which one you want. If you pick Charmander, you'll get Suicune, pick Bulba and you'll get Entei and pick Squirtle and get Raikou.
And Emuritto, it doesn't matter if the dog knows Roar or no, beacuse it'll flee anyway.