Be they anime, manga, Western animation or video games, your favorite characters are not perfect and neither are mine.
Gretel of Otogi-Jushi Akazukin was one of my favorite characters back in 2006. But as I've become more aware of things like character development, I've come to realize that she's not that great. I find it hard to rationalize how smug she behaves when she's an antagonist with this sweet little vulnerable flower who only wants to be happy with her brother.
And that's another thing. Her character is almost entirely defined by her love and dedication to her brother, and one of the "On the next" preview lampshades this by asking her various questions, all of which are "Onii-sama". She has to be stopped when she tries to list him as a hobby. Yea. > >
Kari Kamiya/Hikari Yagami of Digimon Adventure was my favorite female anime character back in the late 90s-early 2000s, and she was the reason I got into the series. The episode where she gets sick endeared her to me and lead me to watching the show itself. But even back then I could look back and realize that she had absolutely no flaws. She's just a wonderful, selfless and pure character with not much else going on.
And now my favorite male character from back in the day, Hiei of Yu Yu Hakusho. I used to think he was the coolest thing, but now that I'm much more interested in good characterization and development, I realize that this guy kinda sucks. He's incredibly OP, and it's super jarring having him go from a one-note arrogant villain to being a cold and collected anti-hero. He doesn't get much development at all and aside from when he was a one-note villain he pretty much never loses a fight.
Goku of Dragonball Z is a pretty likable character, but we all know he's not perfect by any means. If he were at least a flawed character who develops it would be better. One of the most disappointing things I've heard about Goku is that much of his heroism was entirely added to the dub, and Akira Toriyama was disappointed with that. Apparently he wanted Goku to not be as moral as your typical protagonist, so things like him letting the remorselessly evil Vegeta escape just to get a chance to fight him again really makes sense.
Goku's love of fighting is apparently his main flaw, but as a protagonist in a battle shounen (and one that glorifies him above all other characters except maybe Vegeta) there's no way to properly criticize this and have him grow out of it, especially when he does stuff like abandon his family to train some ten year old village kid.
Sakura Kinomoto of Cardcaptor Sakura is often blamed as being the original moe character and the cause of its spread across anime. Not a fault of her, but at least they did it right the first time. The only things I can really say about her are that she becomes a lot more innocent and naive in later episodes and that it sometimes baffles me when strange things start happening and she doesn't immediately suspect it to be a Clow Card.