Let's face it, we all had to start somewhere with our writing. It's not surprising that a few of our characters are not up to par. The dreaded "Mary Sue" that was mentioned in Ran's post about "Killing Your Baby" is considered one of the worst offenders of bad writing. But is it all bad? Let's dive in.
Tone it down:
The standard definition of a "Mary Sue" is someone who dominates the spotlight in the story and are almost perfect. He might face a problem, but breeze through it without fault, or she might always be the object of affection of every member of your story. These are common mistakes, and easy to fix. The issue with "Mary Sues" comes from a writer loving his or her character too much. We want our characters to succeed, especially when their success is a key to the climax. However, if they have succeeded at everything up to that point, there's no exciting climax. That being said, we can certainly fall into the opposite, where our characters fail constantly, but succeed at the right moment. I call this the "stroke of brilliance" character, where it seems they have received the information out of nowhere.
I reference Power Rangers (and other Sentai shows), not for it's plot, but for it's episodic climaxes. There are three in every episode, and they are all the same.
1.The episode monster shows up, after a battle with Putties, causing the Rangers to morph.
2.The monster grows, causing the Rangers to summon the Megazord.
3.The monster gets a leg up on the Rangers, causing them to use the Sword.
Final Fantasy Unlimited had the summon bullet from Kaze's Magun, and Samurai Pizza Cats had Speedy's "magical Ginzu Sword." How does this apply? Well let's say your character is in a bit of a pickle. She's approaching some problem, and is doing well, however, something goes wrong, and she has to overcome that problem as it arises, causing her to grow as a character. This is a speed bump for your character, and while simple, brings the character back from "She can do anything" to "She's talented, but not perfect."
Send them packing on a Guilt-trip:
Some Mary-Sues feel no remorse or guilt for their actions. What they are doing is right, and their cause is just. These are those characters who are blessed or "chosen," and they are called upon by a higher power, human or otherwise. Some of you may recall this being brilliantly parodied in "Blues Brothers," where Jake and Elwood are, in fact, on a "mission from God." They cause car pile-ups, crash through a mall, cause millions in property damage, but don't seem to be at all affected by it. To counter this, make sure that your character has a point in which his or her mission is proven to him, and why he is on the right (or wrong) path. Maybe it's after he questions his mission, like Cecil from Final Fantasy IV, or perhaps it's a final discovery after seeing a colleague's view, like Magneto.
Give them a fair disadvantage:
What I mean is, make them succeed, not surpass. Magic powers, Superior Intellect, and Weaponry may give your character an advantage over their enemy, but much like the first part, make them use every aspect of their character to eventually surpass the enemy. I'm a martial artist, and I've always been taught that a weapon in the right hands is deadly. However, the weapon by itself is harmless. Spikes on the ceiling are great decor in Mortal Kombat, but they turn into a weapon only when a character exploits them. This is the key to many "hand waves" in video games. The characters automatically know how to use all their weapons and powers, even if they have never picked one up. A case can be made for leveling up, and now they do more damage at level 2 than level 1, etc. But you can change the weapon and not suffer a penalty. I play in a weekly Dungeons and Dragons campaign, and the character system to it is very robust and useful for making fantasy characters. Proficiency is a key element, and if your character is not proficient with a weapon, they will suffer a penalty. Sure anyone can swing a stick, but that won't help unless the person knows the ins and outs of using that stick. More realistically, anyone can shoot a gun, but if they don't know to shoot a gun properly, they may end up injuring themselves with the recoil, and most likely missing.
This is the case for Magic as well. Taking the famed "Magic Missile," which never misses, out of the picture, let's explore where magic can go wrong:
1.They have no effect on the enemy, and the character doesn't realize this.
2.The magic can be harmful to the user. (Fire is hot, yo.)
3.The magic can be harmful to the user's colleagues. (Blast radius in D&D can take down other party members)
4.The magic can be harmful to the user's surroundings (i.e. Wheeler from Captain Planet getting yelled at for saying "Fire" when they are in a plane.)
5.The magic can fail due to inexperience or stress. (Chuck from Chuck cannot "flash" on something when he is panicking.)
If one of these things happens, how will they use their power in a different way to still win the battle?
Then there's intellect. Characters with superior intellect seem to "just know." Mary-Sues with superior intellect seem to "just know everything." If your character knows something very well, perhaps they can be thrown into a situation where they might not know exactly how things work, but can adapt it to what they are good at. I will call this the "Scotty Approach." In Star Trek, when one character, usually Spock, throws out a bunch of techno babble, and Scotty, being the one person who can take the jargon and translate it into real words, comes up with a simple metaphor. Let your character do that for himself, or have another character do it. This way, you take your him from being unrealistically intelligent, to being a problem solver, which is believable even with superpowers.
Finally:
A Mary-Sue character doesn't mean that it is badly written. The key is in the writing. Sometimes, a Mary-Sue can be anything but cliche. However, if you do find yourself falling into the same traps with writing a character. Keep in mind their goals, their beliefs, and how you can use those parts of your characters, and not just the characters themselves, to build interest in both them and the story.