Trials plot is fairly coherent, the partner aspect only enhances the plot of your lead character since you'll get more scenes with all the characters involved with it. Trials plot is actually three separate stories that are all happening at once. Even if you don't have any character from one of the plotlines, you'll still meet them and get references to it, it just comes across as a background even to your playable cast. The story is fairly coherent, even with the fan mod if you ask me.

As for Romancing SaGa 2, it's story is more of a framing device that ties together a bunch of smaller stories. It's unique premise is that the plot is a generational story with multiple rulers of Avalon pitching in. The main that ties it together is the revival of the Seven Heroes and their various schemes to send the world to ruin.