It is essentially the protagonist's story you're writing about and thus, he/she must have certain issues that the reader could relate to. Such as taking the bus or driving the car to work or take on the bad guys in a battlefield or sneak into the fortress. It's the choices the protagonist makes, rather than the best of his abilities (indeed maybe the lack of his abilities) which makes a charcter who/what we can love and cheer to.
Oh gods and freaks, I think I subconciously quoted JKRowling's Dumbledore of COS 
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But still, the system works. The character grows, he loses his abilities and makes different choices. You question what if he still had the power and then which way would it force him/her to do the best thing or the right thing.
Indeed, I plan to make my character with super-potential and super-strong but her choices restricts her from acheiving top level. Not to mention getting crippled socially, physically, magically and emotionally (in that order). But remember, what makes a book is the characters. Plural. There are others that would support my protagonist along the way, those she had helped before. They wouldn't want her to give up no matter how much she just wants to lay down and disappear.
So it doesn't matter how tough/weak your protagonist is. Preferably, the tougher he is, the more people needed to bing him down. He could be a god with phenomenal cosmic power but it still comes down to either sacrifice his family/friends so their pure blood can heal the planet or rescue them to a temporary heaven and risk bleeding reality to the demons. It's the walk that goes with the talk 
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I came across this while writing. In the world I'm writing, there are six types of abilities: Corporeal (strength, flight, intangibility etc.) Elemental (able to control earth, wind or fire.) Mage (able to use magic) psychic (telepathy, oracular powers) Spirit, which is the extremely rare ability to use one's own (or another's) life force and Wild, which is anything that doesn't match the other five abilities.
Now, when/if two of these types mate, the child normally takes on either of the traits of their parents, never both. Hybrids are a rare thing. That being said, my main character is a hybrid and posesses three of the types: Psychic, Mage and Spirit. But because he is a hybrid, he is considered to be a bastard by the Mage side of his family, is recognized but not officially protected by his psychic family, and the others think he's too dangerous.
So the main character is ostricized, not taken seriously, and ultimately shunned, which has both stunted his growth and limited his knowledge and control on his powers (especially magic)
So here's a lesson to all, if your character has too much power, beat him down a notch or two to teach him humility
