Aha! I was totally right! Radiant Historia's two timelines are building upon one another almost entirely in tandem. There's still challenge in figuring out when to finish what sidequests, but the main plot is unfolding around a reciprocal building of the two timelines.
What leads me to say this?
I needed to progress down the soldier timeline to learn sword dancing to progress down the special agent timeline. Now, to continue down the soldier timeline, I need to learn some sort of "Keen-Eyed" technique in the special agent timeline.
It's good to be right!
Though, this might mean that there is only one boss to the game. This is where the spoilers come in...(after the jump cut).