Well, in short, Y is separated from RB by anime references, in turn, C is separated from GS by its history. RB and GS are part of the "original story" of Game Freak. The Sevii Islands connect FRLG with E, not with RZ, therefore, they separate from that line. In E, Steven is not the champion, which propitiates his travels around Johto and Sinnoh, these trips are only mentioned or seen in HGSS and in PT, therefore, RZ and DP separate from the longer story. HGSS is a direct sequel to FRLG. In BW, Cynthia talks about PT, not DP, therefore, BW and BW2 join that line. About the Mega-universe, in LGPE Mina's personality is the same as in SM, and considering that Game Freak usually gives more importance to improved editions, these two separate from the main line.