It's a pretty easy choice of Cyndaquil for me. Meganium, to put it plainly, is one of the worst starters ever. Feraligatr is a legit Pokemon now that there are water moves that utilize the attack stat, but for playing through the game you still need a Surfer and Feraligatr's SP.ATK is too low to be good with that, not to mention Ice Beam for Lance. Fire is also a much rarer type (pretty much your only other legit option in GSC for fire was Magmar, since Fire Stones were too impossibly rare to make Vulpix and Growlithe worthwhile, and Houndour wasn't catchable until you beat the E4 and got to Kanto). There are plenty of other solid water options though, noteably Lapras, but also Slowbro/Slowking and Poliwrath/Politoad.
Aside from all that though...I just like Typhlosion the best.