Pretty sure Charmander is faster if you get every 88/94% range and don't miss on E4R1 and E4R2, but of course these are the worst places to take those risks.

SQUIRTLE/MEWTWO:
- Faster Brock split
- Much faster Rock Tunnel
- Faster Route 25
- No Brick Break detour
- No Charcoal detour
- No Dragon Claw detour
- Weaken stuff with Bite (flinch chance)
- Can save 3 more candies for pokes
- Overall less risk, especially in the late game

CHARMANDER (SOLO):
- Much safer Brock split
- Faster Route 3/Mt. Moon
- Much faster midgame
- Much faster E4R1
- Faster/safer Rocket Warehouse
- Faster sidequests
- Can Master Ball something (Onix, Electabuzz, etc.)

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E4R2 COMPARISON (CHARIZARD VS. MEWTWO)

Master Ball				-43
Cerulean Cave money		-2
E4R2 money				+3
Intimidate slave		+5
Dragon Claw				+17	
Overheat				+16
Lorelei					-100 (-78 Blastoise)
Bruno					+20 (+27 Blastoise)
Agatha					+3
Lance					+47
Champion				0 (+16 Blastoise)
TOTAL					-34