Some ideas I had for super powers.
Electricity Blast: Become the Beast of the Midwest with this new ability. (Fat side-kick not included).
Nano-Swarm: Incinerate your enemies with a cloud of deadly nanites.
Infection: Turn a crowd of people into violent crazies; and overwhelm both law enforcers and gang members with a tide of flesh.
Telekinetic Push: Push objects, people and vehicles with your mind.
Telekinetic Grab: Grab people, objects and vehicles.
Gravity Blast: Temporarily distort gravity.
Fire Blast: Unleash your pyro-maniac.
EMP: Prevents tanks and APC's from firing their weapons for about a few seconds. It can also be used to sink boats or destroy aircraft
Parkour: Scale buildings, slide across cars, jump medium sized gaps and make it a general pain-in-the ass for the police.
Neon: Take down your enemies with this fast-action ability.
Super Strength: Pick up objects and vehicles (or vehicle gibs) and use them as improvised melee weapons.
Ice Blast: Freezes objects, vehicles and people which in turn makes them easier to kill or allows you to get out some hairy situations.
Rock: See that chunk of concrete over there? Well you can use it as a makeshift riot shield or you can shatter it and send shards of it flying towards your foes.
Finishers
These are large area of effect abilities that requires you to kill a certain amount of enemies before you can use it.
Breakdown: The Boss grabs his\her head in pain, shortly afterwards a large blast of white energy surrounds the player and destroys everything in the area.
Eruption: The Boss bends over and shoves his\her fist into the ground, sending shards of concrete, shrapnel and pavement all over the area.
Life Force: NPC's, objects and ground vehicles are pulled towards the player and are swiftly drained of all their HP before being violently thrown outwards.
Blackout: The Boss sends out a massive EMP pulse that permanently disables vehicles in the area, destroys helicopters and shuts down all lights in the city.
Perhaps story-wise the Saints use the time machine to kill Zinyak. This restores the Earth but it also causes a time paradox where the Boss ends up getting captured by a new version of the Ultor corporation ran by Dex. The Boss wakes up at a certain Ultor research facility near Mt. Clafflin, but not before discovering that Ultor stole some of the tech from the crash-landed Zin Mothership (covered up as a failed military aircraft) and used it to give him\her superpowers and then tried brainwash him\her into an ultimate weapon. Of course the Boss escapes but not before discovering that in this new reality many of his old lieutenants have never met the Boss, are rotting in prison or work for the local law enforcement agencies and that Ultor alongside STAG have put the US into a stranglehold.