I have all sorts of oddball opinions on this. Anything I post is just what I think, and applies only to my own fanfics, so don't take it as me putting down anyone else's notions.
I don't like the idea of the Fraggle Five pairing off. It would divide them and change the nature of the group. They have a wide mix of personalities, and they function well as a family already; I say let 'em stay that way when they grow up. After all, what evidence have we seen that Fraggles marry?
Of course, there will be pairings of various natures, romantic and non, within this group. Most obviously, Red & Gobo, Gobo & Wembley, and Red & Mokey, but also Mokey & Boober and Boober & Wembley. I don't include Sidebottom as a character because I like to think that later on Boober stopt trying to deny the basic fact that fun is fun, so Sidebottom doesn't need to separate himsels from Boober and act out.
As for Lou and Tosh, I think Lou is just Wembley's good friend, but since nothing really story-worthy happened afterward involving her, we never saw much of her again. Tosh seems to have been an adolescent crush for Boober. Remember how Gonzo fell in love with Madeline Kahn on the basis of one compliment? I see something similar happening with Boober. BTW, this wasn't only in "A Tune for Two" - in "Gobo's School for Explorers" Tosh was clearly the teacher's pet.
The Storyteller & Matt: I fully support this! If only I ever found a way to work it into my stories. Shoot, there's a story in the idea of The Storyteller finally getting Matt's attention. Given how oblivious Matt is, that might take a bludgeon.