I started with Totodile the first time, Cydaquil the second time and Chikorita the third time. Totodile was a fairly good choice, but because of the Red Gyarados you get later in the game, I wouldn't choose it. Cydaquil was just a boss for me and I finished the entire game in <24 hours. Chikorita posed a challenge to begin with, but I liked it and I finished Johto in 48 hours.
This would definitely have to be Totodile. I loved Cyndaquil in gold in silver but Totodile was awesome. Normally I would do Cyndaquil but with GTS I'll probably get him with that. Another reason to do Totodile is I love Feraligator (Probably my favorite water type besides Kyogre). Sorry Cyndaquil but I really want Totodile.
I used Cyndaquil, because I've always used him in Johto. If I ever decide to also buy HG I guess I'll go with Totodile. But I'll probably pick Cyndaquil in the beginning and then just breed a Totodile in my SS >_>
I wavered a long time between chikorita and cyndaquil. Finally I chose cyndaquil because I like his evolutions better. And then it was pure pleasure leveling him up at the Sprout Tower and the Azalea Gym