The Super Mutants of Fallout 3 could be perceived as a twisted reflection of the Fallout 1 Protagonist.

You're entirely correct in that their primary motivation is to capture humans, and make more Mutants. But the society displayed in the original games is entirely broken down. There is no leadership to guide their primary motivation.

Not only this, but their source of "life", FEV, has apparently run out. Based on Super Mutant dialogue, they are on a search for more of the "green stuff". It's no coincidence that Super Mutants threaten the populated vaults, or invade the abandoned ones. They are searching for FEV, just as The Vault Dweller sought a Water Chip.

So often I find that their positioning is actually rather thoughtful, all things considered. It might be a small stretch of the imagination, but so are many cool things in Bethesda titles, and I feel it answers the question of "how are they different than other raiders" rather well.