I'm going to speak on some 'esoteric' powers -- powers that exist outside of frameworks, or don't seem to have a simple place in an MMO.
Stealth powers -- like invisibility, or facial shapeshifting, or a disguise kit -- require a perception system in order to defeat them. It would be nice to have a perception system for stealth-oriented missions, or missions where a stealth character would have other options to complete a mission than just running in and laying down the smack. Seems like this sort of thing would have to be coded into the game from the start, as it's too big an option for an expansion...
Phasing -- the ability to move through objects -- requires that there be objects to move through. Walls and doors that aren't just places the map doesn't exist. Locked boxes an intangible character can just reach through. X-Ray Vision would require the same -- objects to be seen through. And there have to be other methods of accomplishing the tasks performed with these powers. If there's a wall in the mission that a phasing character can just move through, another character needs some way to destroy or deconstruct said wall. If there are boxes a character with X-Ray Vision can just look at to see the bomb inside, other characters need bomb detectors (or the ability to withstand a bomb blast when they rip the lid off the box).
Water Breathing -- I'd love to see underwater zones, where powers like water breathing, super-swimming and Command Fish could be used. (I'm not an Aquaman fanboy, I just believe in empowering those who are.) But if your character doesn't have water breathing, then what? SCUBA suits? Air bubbles? Survival suits? As I said, I'd like to see underwater zones, and people who choose to take underwater powers should get more utility out of them than people who have to rely on Professor Power's Patented Water-Breathing Apparatus Device.
Life Support -- Having your own air supply (or not needing to breathe) could be used as a defense against gas attacks; having a nonhuman physiology could make poison attacks less powerful against you. It's one power that you have to take, but it can reduce or even eliminate element-based attacks against you.
Super-Senses -- they tie into the Stealth/Perception idea above. But I'd like a Low-Light Vision power to enable me to be able to see at night as well as I could in the daytime. Most games, when it gets dark outside, you can't see as well, and that annoys the crud out of me.
Stretching -- there's lots of comic-book characters with it. In my eyes it should be its own powerset, with attacks (stretching a fist to attack someone at range, or turning into a giant ball, or forming yourself into a rubber band to throw rocks at a target), defenses (you're pliable, which means you dodge attacks easily, or your rubber skin resists damage), and movement (stretching your legs to give yourself stilt strides, or just bouncing all over the place).
Shapeshifting -- another powerset. Movement forms (cheetah, eagle), attack forms (wolf, gorilla, elephant), stealth forms (hummingbird), aquatic forms... this will need a lot of additional art resources, but I'd still love to see it.
Duplication -- the ability to summon another entity and fight as your own team. This may be an exact copy of your character (and if I had that ability my next character would be a clone of Tomax and Xamot from G.I. Joe), or a completely different person (a robot drone panther to back your fighting space ninja up in combat). Going to need A.I. to handle the dupe, plus some balancing... you and your dupe shouldn't be as powerful as another character, but taken together you might be slightly better, in some ways).
Anyone have any other ideas for powers and powersets they'd like to see?
"My attention span doesn't wander. It takes long trips to exotic locales where it meets strange women that leave it crying and broken in the hot, hot sun."