These are what we call the 'YMMV items.' Things that some people find in this work. We call them 'your mileage might vary' because not everyone sees these things in the same way. This starts discussions in the trope lists, a thing we don't want. Please use the discussion page if you'd like to discuss any of these items.
God-Mode Sue: Gryphon, Gryphon, Gryphon. This particular Author Insertion is immortal, superbly skilled with just about any weapon you care to name, plays guitar with two highly popular bands, can cut anything in half with a sword, can pull power armor out of hammerspace, is a master designer of spaceships, and sleeps around with multiple hot anime chicks, including his own best friend's girl at one point. In addition, he previously was in charge of the galaxy's most powerful military force, and has 'only' stepped back to commanding the galaxy's most powerful law enforcement organization.
He gets a pass for mostly only showing up in "harried manager" or "comforting father" modes in stories not specifically about developing his character.
At least he started with immortality, so he could spend a few centuries building that list. Yes, even the multiple hot anime chicks.
Some Anvils Need to Be Dropped: Time and again, Undocumented Features shows us that redemption is always possible, even for those who are perilously close to the Moral Event Horizon. And often, all it takes is for the villain to choose to walk away and try to make amends for their past mistakes. Moreover, forgiveness can be difficult, but being able to forgive is a good part of what makes the characters heroes. Without forgiveness, the galaxy would fall into chaos — or perhaps not exist at all (just imagine the consequences if Gryphon and Kei hadn't forgiven each other after the Exile). And most of all, they show that redemption and forgiveness are freakin' cool.
Ultimate Showdown of Ultimate Destiny: Fortress Maximus vs. Surtur. Imperial Star Destroyer vs. the Macross. The Big O vs. an Evangelion. The list goes on and on. Got a favorite? It's probably here somewhere. Or will be.
Unfortunate Implications: This one tends to start flame wars, but it has not escaped people's attention how many of the female characters tend to end up judged by who they marry and who they give birth to as opposed to their other qualities...
Wangst: The main weakness of the early Core stories, especially Kei and Yuri's disappearance in UF1, most of the plot of UF2: The Long Road that resulted in the entire cast becoming immortal, and the downfall of the WDF in UF3: Out in the Cold.