Well, I think that we can divide these "Ubermensch" up into categories:
Solo-Ubermensch: The hero works by himself, with little support (except, perhaps, "back at the base"). The typical solo-superhero approach. James Bond. Superman. Batman. Spiderman.
Ubermensch w/ Support: The hero does most of the work, and is the focus of the plot, but still needs his friends to get the job done. Neo. Luke Skywalker. Paul Atreides. Rand al'Thor.
Ubermensch w/ Plot Limitations: The hero is vastly powerful, but is not the "main focus" of the story, or has another limitation. Gandalf. Aragorn. Professor X. Yoda.
Non-Ubermensch: The character has extremely powerful abilities in one area, with conditional limitations and very significant weaknesses, and is merely another member of the team. Data. River. Wolverine.
I think that it's the second type that irritates people the most, because they expect them to be more like the third or fourth type- more limited, and less focused. They don't want to see the other characters as merely spear-carriers (though I'd certainly say that Morpheus, Han Solo, Alia and Nynaeve are much more than spear-carriers!) The first isn't as irritating because all the other allied "untermensch" are offstage- and the third and fourth categories show the weaknesses that those in the first two lack. (Though some might think that the difference between categories three and four are superfluous, I disagree. Category three ubermensch are those who still seem to be above humanity in many ways- what flaws they have are relatively small. Category four are often seriously lacking in some areas, and typically only have one or two exceptional abilities. Data is superintelligent and super-strong, but the driving motivation of his character is that he wishes he was human- and can't truly understand humanity. Wolverine is tormented and unpredictable, and aside from being a tremendous fighter, doesn't seem to have many other exceptional abilities- far from a perfect superhero, anyway, and not really a solo operative. River is a psychic and a prodigious combatant who seems like a fragile, crazy little girl the rest of the time. None of them are really "ubermensch" in my book.)