I don't understand that comment, what says a sequel has to use the same mechanics at all? Double and Tripple techs if anything were included as a nod. Through the entire game right up to the final battle, Elements are the focus, not combo attacks.
That stance is exactly one of the reasons why I think Cross in underappreciated. It's not Trigger version 2 and it was never designed to be, fans going into it expecting that set themselves up for a fall.
As far as your point about the plot, I would imagine you're talking about the one scene is Chronopolis where Chrono, Lucca, and Nadia are reaming out the party as they head toward Miguel. I think you're misinterpreting that scene. It's ruled out very quickly that the images of those three are merely remnants. When you talk to them again at Opassa, notice how different they are?