It's nice to see people who still tries to appreciate the story instead of just rushing through them. Part of the reason why official Pokemon games are so ridiculously dumb now is because of impatient people who rushed through the story just so they can start doing pvp battles. So now official games get less and less content (dex cut, no more various battle facilities, and a weaker story), just so that those people can get it quickly done and over with and can focus on just pvp. Which is boring.
Anyway, back to PRO. I never really feel it's weird back then, I just think it's amusing that we have this reference and that reference, and I really enjoy seeing all those references. But now that I think about it after seeing your post, maybe at some parts the story would appreciate a rework. I couldn't really pinpoint any though, it's been years since I finished Sinnoh story so it's been a while since the last time I experienced the story, haha. And it looks like Sharktooth is indeed going to try doing something with the region stories after Astrella is done, so that's nice to hear, I guess.