I just started playing again after a few years I played when it first came out and dropped off before johto and I’m wondering how rare the gen 2 starters are? So far I’ve seen and caught over 50 charmanders/ torchics/ bulbasaurs/ mudkips/ squirtles as well as several of all their evolved forms but I haven’t encountered a single gen 2 starter. Cyndaquil has always been my favorite and I want to get a typhlosian. Anyone know of any specific areas where they are more likely to spawn?
Your best bet might be events
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Maybe with a bit of luck it gets boosted (also boosted shiny) on the December community day recap. Let’s hope so!
In the last three weeks I had the sensation that, at least in my area, there are spawning all type of generations and evolutions. It’s like Niantic wants to give you a chance to collect everything from all seasons.
Gen 2 Starters were removed from the list of nesting types either late last year or early this year when they shook the nesting types up. Sadly for me Machop got cut from the list as well.
This makes them harder to find now outside of a themed event.
Your a couple of weeks late as all 3 Gen 2 starters were popping up often but they are back to un common again.
June Research Task “Power-up 5 Pokémon” reward encounters are the Gen 2 starters: chikorita, cyndaquil and totodile. 
Just be patient,
Every week we have another event and every 3 months we have a new seasonal event. Every pokemon will have boosted spawns at some point in the near future.