Invisibility: Another inherently fun power is invisibility. Developers fret about this a lot, because if a game has invisibility that means that every dungeon has to be designed with invisibility in mind. Important guards need to be able to "see invisibility" so they can keep players from just tromping through the whole dungeon without fighting anything. (Nevermind that this is exactly what the player expects invisibility to be good for!) Most games that give players invisibility go out of their way to dramatically limit its usefulness in PvE combat. But as long as there are still enough times where being invisible "pays off", it's a fun power for players to have. In EQ2, it's a great way to go AFK, if you turn invisible, only a few of the wandering monsters will be able to detect you.
Flight: The ability to fly is just inherently fun. You don't even have to work at it, it's just fun. But it's not so easy to add. With flight, players can simply hop over those impenetrable mountains, skip the ambush up ahead, and go right to the boss. It takes a lot of careful planning to make flight a viable, but still useful and fun, game power.
An even bigger problem with flight is the engine requirements: most MMO engines simply can't do flight very well. When you're up in the air, you can see a lot further, which means a lot more scenery has to be rendered, which means the client engine needs to be that much more robust.

(flight in City of Heroes)
City of Heroes has flight, and it's one of the most fun things about the game. They don't cheat people out of it, either flight really is often a useful shortcut to solving problems. This makes players feel clever. World of Warcraft has flight for its new expansion-pack areas.
Many games have "flight on rails" as a travel method griffons in EQ2 and WoW, for instance. This isn't the same thing at all, though you have to solve some of the same tech concerns in order to provide it. I will give EQ2's version kudos, though, because you can jump off your griffon at any point in the travel. That gives you more options for getting places faster, and makes it feel less like a really long, unskippable cut-scene (which is what WoW's griffon flights are). Of course, at low level, leaping off a high-flying griffon is basically a suicide jump...