I always choose the fire type, so in your case, Charmander. When he learns flamethrower, slash, fly, and fire blast... There is an enemy, whip out your Charizard pokeball, there WAS an enemy.
Charmander does make the beginning of the game tougher though, but I always train to level 20 in the first patch of grass, so I rarely have any problems (ya I know I'm a freak).
Cyndiquil is THE choice to make in the 2nd gen though, because when he becomes Typhlosion, he can learn Thunderpunch, which really helps on the Champion's pokemon, as well as your rival's Feralligatyr (don't know how to spell that), as well as any pesky water pokemon you may come across on your journey to becoming a pokemon master.