Question

What is the best starter for in-game playthroughs in GSC?

Answer 1

I think Totodile is the best. It learns ice punch and surf (high base power, STAB, and useful HM move) relatively early, while Cyndaquil is stuck with ember until level 31. Feraligatr's higher physical attack also lets it use return to OHKO opponents that have high special defense or resist all of its special moves.
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Answer 2

For me i'd go for Typhlosion because it has higher BST than other Johto starters

Typhlosion (M/F) @ Charcoal
Moveset:
Fire Punch / Flamethrower
ThunderPunch (Water and Flying coverage)
Earthquake (Ground, Fire, Rock and Electric coverage)
Iron Tail (Rock and Ice coverage)