On the topic of starters, I would also put my viewpoint regarding them (on those whom I didn't talk about to far like Chikorita, Bulbasaur and Charmander).



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Generally moveset wise I don't think Totodile got better nor worse. Special Ice Punch replaced by physical Ice Fang and I think you can purchase Blizzard. Rage and Fury Cutter for Whitney is gone and probably wouldn't work due to Cute Charm Clafable to set up, but you got physical Bite and later get even Crunch for an even easier time against Morty. Stat experience is gone but you get, while late, physical STAB Waterfall.
Feraligator to me was already a pretty good choice for a Starter. It is Water Type who tend to have good coverage by nature. While the first evolution is late, the second evolution is the earliest of all Starter Pokemon and it gets a lot of good moves for Gen 2 standards for a playthrough.
So to evaluate I often look at the main competition for what you could use as a replacement Water Type that would be as good. Sure, Johto has lots of water types that are usable, good even, but not something you would say it fullfills Totodile's roles.
To me that would be Gyarados which is Gators main rival as they are very similar and the shiny one happened to be the same evolution level.
The shiny Gyarados itself is pretty good but in Gen 2 it is I think inferior to Totodile as a Water Type Pokemon you use for offensive purposes. It is still good and can help you as a HM slave.
In Gen 4, Gyarados is flat out better. Gets the same moves except Crunch and has intimidate. Only thing missing is that you didn't get to grind it early. However, you can also use a repel and catch a lv50 Magikarp, Rare Candy it and get your Gyarados that way. The level gap makes up for the lack of exp and I think this is at least enough for me to pick Gen 2 Totodile over Gen 4 one.



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Cyndiquil is a bit of a mixed bag for me and harder to judge. HGSS gives you far more Fire Moves and some earlier even if they are physical now. You can get Fire Blast against Whitney and one shot Miltank. For Typhlosion, you can get Focus Miss as coverage. At lv 57 you have Eruption, the most powerful Fire move with no real downsides when you are at full health.
Gen 2 gives you TMs for STAB Fire Punch and the coverage move Thunderpunch, which generally are plenty for a game like GSC. The bad part is, they are useful when you are fully evolved and Cyndiquil takes the longest for its final evolution and you are stuck with Ember until lv31 where you can replace it with Flamewheel.
In that regard, Cyndiquil did get better. In terms of alternatives, you can get better Fire Types now. In Gen 2 until postgame, you could pick Growhile who cannot evolve (except in Crystal) until Post-game, Vulpix who cannot evolve until post-game, Flareon (exclusive to Crystal) until Post-game, Magmar (except in Crystal where you can get early Magby) after Suudowoodo, Ho-oh who is Gold exclusive, Entei who you are likely not gonna catch and Ponyta who is end-game. Of these options I think Ho-oh and Magmar are the only appealing candidates, because I don't feel grinding for Entei is worth the effort and I haven't tried Arcanine in Gen 2 because I could never get it.
Meanwile what do you get in HGSS pre-postgame:
- Vulpix (you can evolve it)
- Growhile (you can evolve it)
- Flareon
- Ho-oh (in HG)
- Entei
- Magmar
- Slugma?
All of these Pokemon can learn Fire Blast through TM. So in addition to Ho-oh and Magmar (who can now even evolve to Magmotar making it even better), you can probably add Growhile due to its great stats and Vulpix and pick whenever you want to access their high stats. I would probably evolve Growhile immediately because Fire Blast and Espeed are enough for me. Also Entei looks a bit more appealing due to coming with Flamethrower and being able to just slap Fire Blast on it. I flat out Masterballed the Entei in my current playthrough and so far not regretting it.
Looking at Cyndiquil itself, it got better and probably using it over other Fire Types brings you more advantage. Overall, in terms of competition and surroundings I think Gen 2 was better for Cyndiquil.


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I don't think I need to argue here. You know immediately what is the answer. Gen 3 Treeko is awful. The remakes came out in Gen 6, the generation of Mega Evolution. This buff in itself is already enough to improve it significantly. Let's go further.
Special-Physical split, awful, but now you get Leaf Blade earlier and it is 20 base power stronger. Infinite TMs, you can teach it 90 Base Power Energy Ball. You can teach it Focus Blast which will probably miss but it is more special coverage. You get Dual Chop which gets boosted by Mega Sceptile's secondary stab which is Dragon. You get Detect at lv39 which means it is an option against Slaking. For End Game, getting the Dragon Claw TM brings more value now even if its physical. Also Dig got buffed to 80 Base Power, you can 1HKO the Tentacools now.



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Squirtle I think is still the best starter in Kanto. But generally I think it got worse. TM Ice Beam is harder to obtain, Blizzard doesn't hit as often, no badge boost, Dig got nerfed from 100 to 60 base power, TM for Bubble Beam replaced with Water Pulse costing you 5 base power points.
You do get earlier Bite which is now Dark Type and helpful against Misty's Starmie
I think that is pretty much it.