POSSIBLE SPOILERS... or maybe not...
I think the Christmas expansion is going to be a "required" chapter when it comes to the story of the Saint's. Yes, it's a side story but it seems to pick up shortly after the boss rescues his or her homies but before Zinyak is defeated, and the story in the expansion seems to further change the boss into more of a "hero". When the series started the boss was a monster, a total detriment to society, but as the series progressed they became more of an anti hero and by the 4th game, they just became a hero. The xmas story I believe plays into the evolution, and I think if SR5 picks up where 4 left off, we'll see a boss who actually is a totally genuine good guy. SRIV is also the first Saints game where the boss doesn't kill innocent people, even if the player wants them to because all the civilians are simulations.
If the next game picks up where the 4th left off, things may be really, really interesting. I'd still love to see them use the time machine and accidentally go too far back into the past and have to deal living in a very uptight world, or maybe going back to when the Saints first rose to power and just doing things differently, maybe even actually saving Ayisha so that Gat can live happily ever after. But well, it's way too early to start making predictions.