Alright, so what if we considered Cyndaquil in the context of the second generation, where it originated? Now, firstly, in terms of gameplay, Cyndaquil learns moves like Ember, which would be effective against many early-game foes, Smokescreen, which represents the kinds of moves that make early things that people often struggle on like Whitney fairly straightforward (you prefer using a Pidgey for this, but we're discussing approach and design), and Leer for fairly iffy battles and providing support to others, as well as having synergy with the early promoted or hyped Pokemon like Bellsprout or Mareep, which are effective against early threats like water types. They thus have a decent combination of subtlety and offence, for a Pokémon, and an important place in the game. They also come from an era where the starters were slightly more serious and less 'cutesy' than in further versions. In addition, the 'hype' around them seems interesting, because the game itself isn't necessarily going to be that keen on you choosing a Cyndaquil, which would trivialise a lot of its obstacles. In this sense Cyndaquil is given a sort of baseline personality which other Pokémon might lack.
It also has a decent, fairly obscure evolution in Quilava. In terms of issues, it has a few including that for instance such games could frequently make Cyndaquil's weakness to water-types into a bit of a plot on its own, especially with these types occurring somewhat at random later on in the game (Poliwrath, Kingdra, really most of the Pokémon in Pryce's gym...), along with water stages playing a significant role, making Typhlosion's compatibility with moves such as Thunder Punch seem quite important (if you really want to evolve Quilava, ugh.), if it isn't to be sidelined or a bit of a slog for significant portions of that sequence. Nonetheless, as Pokémon go, it's quite a decent one and it doesn't seem to deserve the distaste in that context, whatever they may have done to throw random features at Pokémon in later games. In any case, it might be worth considering whether the Chikorita line having seemingly significantly less difficulty with gyms despite having to face less-than-favourable places earlier on might not reflect on the game being slightly different or on the line's significance to such, especially given the early availability of rock-types here compared to Red/Blue, which again seems to complement them. Nonetheless, Cyndaquil is certainly unique and differentiated in a few ways, complementing some of the later aesthetic of the game, the black-outs and dreary locations, etc.