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I went for Totodile for my Soul Silver game because I tried the two other starters in my Gold game. I just wanted to try a different starter. He's quite strong once he got a few levels in. XD Also, used him in a lot of battles while another Pokemon has experience share. XD
I chose Cyndaquil, which is fairly new since I always choose Squirtle/Totodile/Mudkip/Piplup, generally Water-type starters. I liked water type starters as they are much HM slaves and could learn a variety of moves. I just liked how the Cyndaquil walks with you at early stages of the game (because it evolves later on, so walking with Typhlosion is uhhh... Let's just use the bike).
My preference has been the Water Starter, ever since Gen I Games :D But occasionally I would choose the Fire Starter :D And I'd sometimes choose Turtwig too .. I always hated Sceptile/Meganium xD
After so many restarts since I got the game, I've finally decided to stick with Totodile. I had it before when I started over, but unlike DPPt, HG/SS allows you the false start over, so when I tried to save it wouldn't let me. Or at least that's what I like to call it anyway. I've pretty much had each Johto starter at least once so far though.