A few thoughts (still haven't gotten around to testing) on the starters.
In terms of Gym matchups, Totodile beats the brakes off Cyndaquil and Chikorita both. Rage can crush Falkner, Bugsy, and Whitney, Surf can hit Morty very hard, Dig + Surf destroys Jasmine, Surf beats Piloswine (Seel + Dewgong go down to Return), and Clair's Dragonairs eat Ice Punches while Kingdra eats Returns. Dude has practically no bad matchup, Chuck is the closest thing and you outpace and bash him with Return anyhow. Cyndaquil does moderately well against Falkner, roasts Bugsy...and then kinda needs TM support or Flame Wheel to do well against the rest. Fury Cutter/Rollout can take Whitney and Pryce though, Dig can really hurt Morty, and Flame Wheel barring a crit roasts Jasmine.
For the E4, however, Typhlosion can practically solo the members with some healing and PP support between fights and contribute against Lance surprisingly well (you can beat Gyarados and Charizard pretty smoothly and with healing support, can manage one or even two D-Nites provided they aren't really lucky, my logs demonstrate this pretty consistently actually). Charcoal Fire Blast alone can OHKO multiple Pokemon - add Sunny Day in and it can OHKO practically everyone, barring Houndoom, Umbreon, and Muk - they're 2HKOed. Feraligatr cannot do this (at least not without more healing support) and actually has issues with Lance too (all of his Dragons can live an Ice Punch generally, you can upgrade to Blizzard I suppose).
IMO, Cyndaquil > Totodile in the endgame, though Totodile admittedly > Cyndaquil the rest of the time and overall. If the game's divided into three parts (early game, mid game, and endgame), Totodile does better for 2/3 and Cyndaquil does better for 1/3. That said both Totodile and Cyndaquil are pretty good even in the parts of the game they're less good at (Cynda does a lot better in the midgame than previously anticipated for one), so my takeaway is that the gap between them shouldn't be huge, though it definitely favors Totodile again.
Curious to see how Chikorita(F) fares, as that's the one I promised to test. IMO Chikorita should be able to contend against any gym apart from Azalea or Ecruteak, though I don't see him necessarily being dominant like Cynda is against Bugsy or Totodile is against like 4-5 leaders lol. The E4 performance is arguably more worrying as some of them (looking at you, Will and Koga) really don't match up nicely against Meganium.