A lot of the oddities and bizarre design choices about GSC compared to other games can be attributed to the fact that it wasn't really designed to be its own self-contained adventure. The Johto games are more of a sequel to the Kanto games in that back then they were essentially "Pokemon 2", a continuation of the original RGBY. It's not like all the games that came after in that everything from Ruby/Sapphire onwards is essentially a standalone, self-contained adventure and Game Freak designed most of the games from there with the mindset that they want to "recruit" new fans into the franchise with each new generation, showcasing new sets of Pokemon to be beloeved by fans each new gen, and vice versa.
Gen 2 likely wasn't designed with that mentality in mind. As I said, GSC is a sequel to the original Pokemon games, in other words "Pokemon: RBY Part 2", and as such, it essentially operates on the assumption that someone playing GSC already played Gen 1. In that sense, it was meant to draw in familiar players who were already fans of the original games, and wanted more Pokemon content because they loved playing the originals.
The reason Johto mons were designed to be so rare, in my opinion, isn't that the designers disliked the new Pokemon, but that they wanted the new Pokemon in GSC to feel more "special" to players. As I said, GSC being a sequel to RBY means that it's assuming the player is coming in from having played Gen 1, and Johto is a complementary region to Kanto. So as such, it basically treats the player with familiar old Kanto Pokemon that they saw in the originals, and players will be like "Yeah, I know that Pokemon", but then they suddenly find that rare "new Pokemon" that they see, like Natu, Wooper, Heracross, etc. and the player suddenly has a "WOW I found something new!!! This is awesome!!!' reaction to finding it, and give people that amazing rush of excitement when they find a new Pokemon that didn't exist in RBY. Like you found something remarkably new, and it's something you, the player, have found and discovered for yourself. It's supposed gives a sense of having an amazing discovery after being familiar with the original Gen 1 Pokemon. Of course, in hindsight, this didn't work as well as it was intended, but this was likely the specific intention they had in mind with why the Gen 2 Pokemon tend to be so uncommon in GSC and rarely seen in Trainer battles.
This mentality also likely applies to them designing the Kanto segment of the game: some new Pokemon like Houndour, Slugma, Murkrow, etc. were placed there so that players could still have more "new Pokemon" to discover and find when they go to Kanto. Like you go there, and you think it'll just be all the Pokemon you saw in RBY and the Johto segment of GSC, but then you see stuff like Houndour, and it just invokes more of that special feeling of still finding something new you never saw before in RBY.
This also further ties into GSC's weird level curve, which based on my experience it's designed with a bit of freedom in mind in terms of exploration, but the Johto segment I am inclined to believe was meant to be gone through with 3-4 Pokemon, up until the Kanto segment. In that sense, the Kanto segment isn't really a "post-game" in the traditional sense, but is more accurately described as the second half of the game, where you pick up 2 more Pokemon or so to round up to a full team of 6: so stuff like Houndour and Slugma are more "late-game inclusions" to a team that you use throughout the Kanto half of the game up to the Mt. Silver battle with Red. So the new mons here are more "late-game" than post game: the game was likely meant to have Kanto as a "Part 2" of the game, and the game's main story effectively ends with Mt. Silver.
That being said, this was moreso my analysis of what Game Freak was likely thinking with designing GSC, and I think this is the idea they were going for with the new Pokemon: they were meant to be "rare, but special discoveries" to people who came in off of RBY and were playing this for more Pokemon content after the first games. GSC was designed with the mentality that it's a sequel, and therefore is inherently attached to RBY and assumes you know and have played that game. Gen 2 mons unfortunately do end up being more obscure as a result because the general thing with sequels is that a lot of the things in sequels aren't quite as memorable as the original thing when it comes to a series, so the Gen 2 Pokemon and the way they were implemented resulted in them ultimately being, unfortunately, less memorable than the original Kanto Pokemon and the Pokemon that came in generations afterwards.