I think a big thing that inadvertently helped Cyndaquil and Totodile in GSC was a lack of decent Fire and Water types before the postgame.
One reason Squirtle wasn't the greatest choice in RBY (either as the starter in RB or as the gift in Yellow) was because of all the superior Water types you could get later on, such as Gyarados, Vaporeon, Starmie, Lapras, and Slowbro. That wasn't exactly the case in GSC, where the usefulness of most of these Pokémon was nerfed by either the split Special stat (Gyarados, Slowbro), lack of easily available Water Stones (Vaporeon, Starmie), or lack of Ice Beam/Thunderbolt TMs (Gyarados, Starmie, Lapras). Furthermore, the best new Water type, Kingdra, was a trade evolution (and with an item that wasn't even available until after the 8th badge) and possibly even needed to be bred to reach its maximum usefulness (ie. Aurora Beam).
This made Totodile a far more attractive choice in GSC than Squirtle was in RBY. You got it early, it had solid, usable stats, it was guaranteed a good Ice move early on with Ice Punch, and it also had Bite/Earthquake for extra coverage. It also probably did the best against the gyms and E4, overall. Neither of Feraligatr's weaknesses even appeared until Kanto (Surge and Erika), and by then, you likely had other Pokémon to easily deal with those gyms (heck, even Feraligatr itself could do it with Ice Punch/Earthquake).
As bad as the Water type situation was in GSC, though, Fire types had it even worse. Lack of Fire Stones eliminated Arcanine, Ninetales, and even Flareon as options, and Houndoom wasn't available until the postgame. That pretty much left Magmar as the only real alternative to Typhlosion and only in GS, mind you (outside of getting lucky with a Magby from the Odd Egg, Magmar wasn't available until Mt. Silver in Crystal). Sad as it may sound, a Kadabra, Alakazam, or Gengar with Fire Punch was probably the best alternative to Typhlosion.