Joey MacAdoo in the Backyard Sports series. Saying nothing other than corny jokes ("You gotta MACADOO it!") in his first appearance in Backyard Baseball 2007, he was destined to become The Scrappy. The writers somehow thought he and Ernie Steele (who is also corny, but actually realizes he is making bad jokes) should be the poster boys for the series, evolving into a Creator's Pet. Even worse: In one of the few Backyard Books, Joey is the main character.
Within Crisis Core, we have Genesis. Essentially a Sephiroth knockoff, he acts like a loathsome spoiled child, commits numerous acts of murder and violence for no good reason (not even having the Sephiroth excuse of being Ax-Crazy) and is generally uninteresting. Yet, the major events of the game revolve around him and the events of Final Fantasy VII have been retconned to all revolve around having been kicked off by Genesis. Worst of all, Dirge of Cerberus shows us he somehow survives with no ill effects, making him the FFVII series' Karma Houdini. This might have to do with the fact that Genesis was based on popular J-Pop singer Gackt. He only appears to be in Crisis Core to have a Final Boss to fight, since Sephiroth's survival is a Foregone Conclusion.
Final Fantasy XI has Absolute Virtue, a side boss that no one seems able to defeat. Every time someone does manage to find a way, Square Enix goes out of their way to squash those methods to render them useless (and often bans the players who did it). It's as if the developers enjoy using the boss character just to piss off their fanbase.
The character of Mhenlo at times felt more like the hero than the player characters. In the cutscenes, he seemed to do most of the thinking and talking, and he appeared to be..."acquainted"...with most of the female population of Cantha. In addition, that chapter was full of Escort Missions, usually with him as the person who you had to keep alive. (It helped that Mhenlo was actually a healer who was good at keeping himself alive, though.) Fortunately, ArenaNet dialed his importance FAR back in later campaigns and didn't make that mistake again.
Although Lieutenant Thackeray is coming close to taking his place. It's already been revealed that he's going to father an important character in the sequel with fan-favorite Broken Bird, Gwen. However, he was only introduced in the Christmas event, and since then his interactions with her have been seen as ham-handed at best, and outright forced at worst.
Taimi has become this over the course of the living story. There is nothing she can't deduce with her superior intellect, no problem she can't solve by building a magical machine, and even though she is still just a child, the plot is frequently driven by the player character (and ostensible group leader) running around following the instructions she broadcasts. The only characters who ever seriously whether Taimi should be in that role are portrayed as unequivocally wrong and likely corrupt. Fan reaction to her has become increasingly negative, but the writers still can't seem to get enough of her and she is worked into any possible plotline.
Hyperdimension Neptunia mk2 is largely laid out in a traditional Saturday morning cartoon fashion. Two very cartoony and decidedly fairly nonthreatening villains, Underling (her real name is Linda, but everybody calls her Underling) and Pirachu, hinder our protagonists at every turn as they attempt to accomplish their objectives. The game's creators have since acknowledged that the Saturday morning cartoon atmosphere and Underling were probably mistakes. But what about Pirachu, the less popular of the duo, considered to be obnoxious by many fans, and who scored lower than Underling on the official popularity poll? Oh, he's back for the sequel.
The Lord of the Rings Online has Thrymm Redbeard, an original character not from the books. He is a Rohirrim hero that came with the Wildermore expansion. All of the Rohirrim in the area shill him constantly, and when he apparently dies, they all go into a gloom about how no one else will be able to save them. The main antagonist, Nurzum, defeats Thrymm by grabbing him and throwing him about a mile away. You personally are not really allowed to fight Nurzum the multiple times he appears, because he's too much of a foe for you. Despite all of this, Thrymm's only real accomplishments in the story are somehow surviving being thrown for thousands of feet and defeating Nurzum at the end of the storyline. Yes, the character that you're considered subpar against killsteals the main antagonist of the entire expansion while you sit around debuffing him and playing second fiddle.
Rayman: Some older members of the fandom absolutely deplore the Raving Rabbids. There can be little debate about their forcibly changing the Rayman series from adventure platformers to collections of short, bizarre mini-games, pushing all of Rayman's previous supporting cast out of the spotlight, and carrying on their franchise hijack for a large number of games in a short amount of time. Their Creator's Pet status only became more apparent when two or three of them got a playable role in, of all places, a Teenage Mutant Ninja Turtlesgame. Thankfully, the Rabbids eventually split completely from their parent franchise and Rayman's started going on adventureswithout them again.
Aya Shameimaru has long flirted with Creator's Pet status. She made her first appearance in Phantasmagoria of Flower View as a tengu reporter who was investigating the incidents going on at the time. Oh, and she also "accidentally" beat up everyone along the way because she was "holding back" and "not actually trying to fight." This would have been one thing, but she would, in some form, go on to appear in the next four Touhou games, including a Gaiden Game with her as the main character. Her appearance in Mountain of Faith was particularly infuriating because most of the old cast, Reimu Hakurei and Marisa Kirisame notwithstanding, made no appearance in this game... except for Aya, who not only ended up being the level four boss, but was explicitly stated by Touhou creator ZUN himself to have lost to the heroine on purpose.
At her peak, Aya had become so bad that a minor meme had spawned explaining that she had gotten into so many games in exchange for giving ZUN sexual favors (a highly disrespectful meme now that ZUN is Happily Married). However, fanon often portrays Aya as a humorously over-the-top, so-obnoxious-she's-funny tabloid reporter with a penchant for taking embarrassing photos of the other girls. This interpretation of Aya is not nearly as bad as the one that ZUN has saddled her with, and it not only rescued her from the Scrappy Heap, but it gave her almost as many fans as she has haters, making her one of the most polarizing characters in the series.
Sanae as of late is on the verge of coming off as this, as she's been getting many starring roles and generally being shown as being on the same level as the other two heroines. She has also been getting some polarizing character development as some like the new quirky zealous Sanae while others prefer her earlier personality. A sign this may be wearing on the Japanese is that she's started to slip in popularity in Japan. Her absence between Ten Desires and Legacy of Lunatic Kingdom alleviated this, though, with some people accusing one of the older semi-heroines with actually more appearances than Sanae — Sakuya — of being this in turn.
In Ratchet: Deadlocked, Ace Hardlight serves as the Creator's Pet for Gleeman Vox, being over-promoted and having tons of merchandise based on him, even though it's very clear that the audience hates him. After his defeat near the end of the game by Ratchet, the audience celebrated, despite Vox trying to make the defeat look like a tragedy.
In Professor Layton vs. Ace Attorney, Espella Cantabella is beloved by her father the Storyteller and treated with fear by the other citizens. It's said that if someone crosses her, the Storyteller will ensure the culprit gets screwed over by the story.