Go with whatever Pokemon you like best. Squirtle's been good to me for the Gyms, although with Charmander now able to learn Metal Claw, it can slash its way through Brock at least. Both have trouble with Misty, but beyond that, Charmander's good for Lt. Surge, Erika, and Koga -- on a level. Sabrina gives it trouble because many of the apprentices sport members of the Slowpoke line. Then, you've got to worry about Blaine and Giovanni, but you should have Pokemon that can take care of them by that point. Squirtle can't do much for Misty through Erika (although it can resist Misty's attacks), but it does all right for the rest of the Gym Leaders, especially the last two.
On the E4 front, both Charmander and Squirtle may encounter problems with Lorelei because of her Water-type Pokemon, but again, you should have Pokemon for her by that time. I wouldn't use Charizard against Bruno (because of his Onix), Agatha can be taken by either Pokemon, and with the proper TMs, you may find yourself gliding through Lance without a problem. (However, I prefer Squirtle with Lance because of a combination of its ability to learn Ice Beam and the fact that it's got a one-up against Aerodactyl any way you put it. Gyarados may be a problem, but lead with a Pokemon sporting an Electric-type move, and you'll be fine.)
Overall, I'd say go with Squirtle, although Charmander's got its perks too, considering Charizard's better at quick assaults than Blastoise and does fairly decently for the middle few Gyms.
