I would like to see three factions that have the effect of altering the nature of certain powers, giving different missions of course, and affecting PvP trigger conditions. It would also be cool if the three factions all shared the same city.

The three factions would be hero, mercenary, and villain.

The hero faction can't take power options marked as 'vicious' and may choose 'motivated' self buff powers that kick in in certain events, like when they save the lady's purse from being snatched, or fight a NPC or PC villain. Heroes can trigger PvP if they catch a villain in the act, after spotting suspicious behavior. There would be a chance of this every time they come near a villain in the process of doing a villain mission. Hero missions should be more about their personal story and personal character development, using a flow chart so that every Hero goes down different mission paths, increasing replay interest and making heroes alluring to players as a character choice. Each mission would give them a different type of 'motivated' buff for a while, depending on the difficulty.

The mercenary faction has a boost with powers like gizmos and martial arts and weapons (where they can do more 'temporary power' type missions that upgrade said powers for a bit) and has missions that are seedy and roguish and all about personal gain, but not to the point where they do villainous things. The mercenary can team up with heroes or villains, but not both at the same time, and share in the missions from that faction while teamed. Mercs teamed with villains or heroes share the same PvP flag conditions (the Villain or Hero seeking payback is going to get you because you are helping their hated foe, or if you're doing a crime with a villain, you need to go to jail too). Mercs doing missions with heroes would gain the motivated buffs as a reward for completion.

The villain gains a boost with power options that are flagged/tagged as 'vicious', which would give them an edge in darker power themes. Their missions would range from working with megalomaniacs to following leads towards gaining power. For this reason, they would have the same temporary power bonus from missions as the merc, but towards their 'vicious' abilities. Their missions would also be about connections and contacts to gain material power as well, allowing them to draw on crime kingpins and masterminds and other such overlords and despots for resources in exchange for favors. Thus, they wouldn't just be doing missions for xp, which results in the 'grind' feeling, but actually working towards goals like a temporary hideout or access to an item on the black market. Villains can trigger PvP on any hero that has foiled their plots before.

Edit: As far a higher level 'ganking' - you can have it so heroes can only perceive suspicious behavior of characters around their level or higher, and villains cannot totally defeat characters they have surpassed in power, only humiliate them once, until the power level has been equalized again, at which the hero/mercenary can do one 'payback' PvP attempt without the need for a 'suspicious' event to be perceived.

I'm aware the system may be too developed to realistically implement this at this point, but I'm putting it here in case the idea is useful. Also, the idea of Heroes being defeated should involve the standard defeat scenario, but villains defeated by heroes or police should respawn in jail and have to break out, unless they have done a mission for a crime boss or whatnot giving them a variation on the old 'get out of jail free' card. Mercenaries might seek out villain partners in order to get this mission reward as well.