Night/day kind of bugged me (it was there in RSE, but not obvious), berry trees were probably dependent on the game clock, "no breeding" isn't true, it's just only post E4 since there were Pokemon you could get by breeding that weren't on the Kanto dex, No Gen 2 Pokemon makes sense since it was, well, a remake of Gen 1 (and many of them are there post E4 and if they're not there, they're somewhere else in the generation, like Colosseum or XD), No phone was a gen 3 thing (and PokeNav and Vs Seeker were better anyway since you weren't capped on the number of trainers you could seek a rematch with at a time, while you were capped in Gen 2 because you could only hold a certain amount of numbers), no following Pokemon makes sense since that was a Yellow-only thing at that point in time, and lacking Jessie and James was quite frankly an improvement over Yellow (Jesse and James were cakewalks compared to the Rockets they stood in for, really).
Yellow, while fun, wasn't really any different from RB aside from the Pikachu things and mild story alterations to better match the anime. It doesn't exactly deserve to be thrown on a pedestal.
Did you even explore the FRLG post game? It isn't much by today's standards, but it was the most we had in any game up to that point.