Well, considering Chrono Cross both a) eliminated Magus from the game due to time restraints and storywriter brainfarts and b) had to encompass so much more than just the Viper Manor/Lynx's Manor scenario alone, it's not all that surprising that the plot would fail in comparison to a true Radical Dreamers fan. But you have to keep in mind that although Chrono Cross is considered a "remake" of Radical Dreamers, both games have their own unique storylines linking Serge and Kid to the discovery of the Frozen Flame, so naturally they would take different direction. Honestly, I thought the homage to Radical Dreamers in Chrono Cross was more than enough for me (since I had played RD before Chrono Cross's debut in the US), because I was glad to discover the developers decided to make an almost entirely different game, not a carbon copy of RD with flashier graphics and a non-text based format.
You just have to remember that although CC is defined as a "remake," in actuality they're two entirely different games with plot threads in two (okay, three if you want to get all technical) entirely different dimensions. Appreciate the merits of each game seperately, much like the Final Fantasy series, and you'll come out enjoying CC a lot more.
