Well, in opinion I believe that as of the area, Gym, and native Pokemon, Cyndaquil is in technicallity, the best choice. Chikorita, although definetely stronger later on, is NOT good for the beginning of the game. The first 2 gyms are it's weakness, and it does not level up easily. Now I've always picked the Cliche yet nostalgic Cyndaquil, but recently I've been taking a liking to Totodile, and honestly I don't know why. Maybe it's just his always happy, reptillian appearance, but I do like him. Now my plan was that once I got the new game, I would trade off 2 of each starter to my friend, who would then trade them back to me. The last starter I would get would be Totodile. This would not only show my emphasis for my newfound love of Totodile, but it would also mean that I could use Cyndaquil on the Rival's Pokemon.
Anyways that is my opinion. Now I've always thought that Cyndaquil is good for Gold (It reminds me of the warmth of a beating heart), and Totodile is good for Silver (He reminds me of the icy, yet cool feel of Steel).
Also I heard about a few new routes opening up!