The cut-scenes in Treasure games (especially S&P 1 and 2) are mostly there for pacing reasons rather than plot reasons I imagine. Having a break in between the action just fits for most arcade style games like this. I think they also give atmosphere and context, but I don't think Treasure really wants them to be representative of the game as a whole. If you want to have a break neck arcade game, it is tough to pace the game so to not overwhelm players.
BTW I love the atmosphere in charm in Treasure games like Mischief Makers, Silhouette Mirage, and Gunstar Heroes. They aren't trying to be "great plots" and are just there for fun.