Sometimes I wanted to choose Totodile but I knew that I must never do it because that is the choice that leads to evil. Not immediate evil, but evil as a consequence.
If you choose Cyndaquil then your rival will choose Totodile and Chikorita will remain sealed at the pokemon lab forever as it ought to. However, if you choose Totodile, your rival will break the seal and be required to raise and train a Chikorita and nobody deserves that fate, not even heartless criminals. It is always a trainer's duty, and burden, to choose Cyndaquil when given then choice in Johto.
