Character builds based on RIFT's Soul system
City of Heroes goes with classes that have some clearly defined powersets. Champions Online gives players a whole buffet of powers that can be picked from more or less at will. But I don't think either quite get the sense of superheroes because superheroic roles and abilities are constantly in flux. There needs to be a way for the rock-hard bruiser to turn into a shy mentalist after one cosmic event or another, and there needs to be a path for making someone with only a few minor powers just as viable as someone with a spectrum of abilities.
Enter RIFT. RIFT's soul trees are remarkably flexible and do a wonderful job of giving the freedom necessary to have multiple sorts of fire-based heroes without pigeonholing those heroes into classes. You could have a player spending points on a fire-based melee tree and a fire-based ranged tree, or someone who spends point on Fire Melee and Ice Melee, or Fire Melee and several totally unrelated trees. And because of the way RIFT handles it, there's also a viable split between spending your points in one tree, two trees, or even a three-way split.
Obviously, there would need to be adjustments made to the system. I'm not imaging classes, for instance, just a long list of power-based trees that players could invest in, but you could easily divide classes up into general families of powers, like element-based heroes or weapon-using heroes or the like. But no matter what, it's a system that offers a framework for varied heroes while still keeping players from sampling everything on the buffet.
Equipment system of Guild Wars
Most heroes don't really use equipment, and even those who do don't use it in the traditional MMO sense. Iron Man might have a specialized armor for nearly every situation under the sun, but it's not like he beats up some weapons dealers and then gets Repulsor Gauntlets of the Whale as a reward. No, you need an equipment system in which the emphasis is on significant tweaks with a very low ceiling of power -- which, not coincidentally, is what you see in Guild Wars.
These armor pieces may or may not be reflected in the costume, but they do allow you to stop an escalating gear race. Instead, heroes would have a fairly fixed level of stats they could reach, and the key feature would be tweaking those finite stats. That would, however, obviate the rare Guild Wars armor, which is sought after mostly for appearance, unless you also allowed players to craft costume pieces that bore marks of certain extradimensional jaunts in certain high-level areas. So there's room for even that cosmetic sort of high-end advancement.
Social systems of The Sims
Wait, am I branching away from MMOs here? Yes, I am because superhero stories are about not just a guy in tights but a guy in tights dealing with a supporting cast and social obligations. Most MMOs have neglected this aspect of superheroes, but I think it's an area that deserves a lot more attention, and having a supporting cast of real-life friends and family makes the whole story feel more organic.
If you've played The Sims, you know that the relationships in the game decay over time, requiring you to bolster them. Add in some dynamic mission cues and suddenly you get the sense of comics in which a character is trying to deal with a heroic crisis while at the same time trying to smooth over personal interactions. It keeps you on your toes, and it means that even in a very mundane mission, you find yourself having to pause against thugs to call up your aunt and reassure her that yes, you'll be home in time for dinner.
And to add in a little more spice, let's tie this into other game systems. Sure, you might not necessarily like your alter-ego's boss, but if he fires you, you lose access to your crafting facilities and your money. Ignoring your social needs harms you in the game as well. That's part of the balancing act for a hero.
Combat system of TERA
I have a lot of issues with TERA, most of which I presented in my Choose My Adventure series in the game, but I can't deny that the combat was pretty great. It was fast, and it was energetic, and even if it would need some tweaks to work properly in a superhero environment, they would be worth it. This could even map nicely to creating your own sort of hero, with some players preferring a more dodge-heavy style while others block to avoid damage.
Bonus missions of Star Wars: The Old Republic
This might seem a little more random, but one of the big parts of the superhero genre is that heroes don't just rush off to fight a supervillain. Sometimes you help a lady getting mugged. Sometimes you get a cat out of a tree. Sometimes you just help an old lady across the street. The whole point of superheroes in the classic mold was that these were people who just did good things all around.
So give us good things to do. Give us cats to rescue, muggings to stop, little ways to help out people who can use assistance. Star Wars: The Old Republic is good about giving players little bonus objectives under the right circumstances, and that seems like a perfect equivalent here. Sure, you could just foil the villain's plot, and that's worth something. But if you foil the villain's plot, call your girlfriend to confirm your date for later in the evening, prevent two car crashes, and save a kid's balloon before it drifts away?
Now you're a superhero. And the game should reflect that.
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