It may be a bit obvious because of my avatar, but Totodile. Why do I like it?
I was playing my first HG, during mid-2010. I was deciding between the 3, but I eventually went with the gator-no readon, it was random. Since I was really young when playing, I didn't know how to switch out and so I used my Totodile for basically everything. He soon grew into the powerful Feraligatr and soon destroy all.
Here the thing- these guys have the coverage for DAYS. Secondly, here's something I realised Feraligatr has that most starters lack: fairly balanced stats. Of course it's not too balanced, but there's just something for all his stats. He's fast, hits hard, and has the bulk to take a hit. So yeah.
And about the other 2, they are....eh. I started off liking them all, but now Totodile is literally the only one of the 3 that I like. Taking its disadvantage out of the way, Meganium has actually alright stats; fast and decent defences, but it has a bland appearance and a limited movepool. Cyndaquil has a much better movepool, but I am a bit of a mixed bag; let me get you started with my 2 nuzrun Quilavas. The bad Quilava was Flamous from my SS run. Thanks to his nature, he hit like feathers, and was basically fast and thats it. He pulled the team down and as a result I felt no sorrow for his death. But I used a Quilava again, but this time was in my Black egg run. He was very useful and easily redeemed the line for me. Maybe if I continued that run or evolved him into Typhlosion, I would like the line again.
In a honesty though, I pretty much love Totodile too much to pass him up. I will always pick him as long as he is available, no matter what.