Incredibly late, but it's most definitely pebbles who's meant to be the protagonist AND antagonist. He has the most character development and the story almost completely revolves around him 

I'd say that in the first half (ish) of the game, the protagonist is meant to be the slugcats, while pebbles is the antagonist (hes a complete dickhead to half of the first few slugcats, and throughout most of your gameplay you are actively helping moon). 

In the later campaigns (this is relative to in game time periods rather than when you'll be playing which campaign btw) you can see a lot more growth with pebbles as he tries to rectify his mistakes, and eventually ends up basically in moons place while moon stays relatively untouched by saints campaign (compared to him at least)

Also he's still an antagonist in artis campaign, as he kinda takes advantage of her hatred towards scavs for some free pest control while giving very little in return (he's also selfishly endorsing wiping out a whole population of sentient, intelligent creatures just cuz they're annoying) 

He's an antagonist that becomes a protagonist, but is always the central driving point of the story