It’s kinda hard to say when u really get down into the games development cycle. I always assumed the reason for Kanto being roughly half a region in terms of content was due to not having enough space on the tiny game boy color cartridge, and considering hgss added most of the missing stuff in, that makes sense. But apparently before even finishing johto, they were running out of space (which is why johto kinda feels small compared to other regions), but the late mr iwata was able to find a way to compress the data to where Kanto was even able to fit in the first place.
Also gen 2s development was a bit of a mess; not as bad as gen 1, but still more chaotic compared to later gens. But people have combed through the code to find things like the idea for the honey item in gen 4, an undestroyed cinnabar island, and of course the beta safari zone map, among other things. So my guess is they just couldn’t buy more time to put more stuff in; after all gen 2 was supposed to be released in Japan in 1997 I believe, but didn’t come out til 1999 in Japan and 2000 in America. And with the gen 1 not even being out internationally at the time, nintendo might not of been as eager to offer extra help beyond what iwata was able to do.
again hgss added a lot of the missing areas, but by then game freak got their development cycle down pat, had a lot more space to work with and could probably get extra money/help from nintendo if all else failed, luxuries that weren’t a thing while working on gen 2.
overall johto is the better of the two (considering it was newer it’s understandable that it would get the higher quality stuff), but seeing Kanto change over three years (even it was only about half the stuff as before) was still nice even if it was more a bonus thet really only made it by luck.