Interesting thread. I'll give it a go.
The Good:
1). Hard-work/Determination Themes--- One of the things I've always loved about Naruto is how the make the main character have to earn and work everything rather than just have it handed to them on a silver platter. It makes the end result more meaningful and might even inspire some real-life people to work harder. I'm particularly lazy by nature, so when I watch/read Naruto it sometimes makes me want to be a little less lazy lol.
2). NaruSaku's development--- Of course. This should come as no surprise.
I love how many different stages Naruto and Sakura went through, both have periods of being selfish with other and then progressing to selflessness, and how much more of real feel it gets when it comes to real life relationships. I like changing and development to this caliber so I will always praise Kishi for doing this.
3). Sakura's development--- I will never get over how impressed I am by Sakura's emotional development throughout the series. She started with almost zero likable traits, shallow and selfish to the core. But you see her mature over the series into this selfless, good-hearted, realistic, and mature female character that seems almost like a different person. The way Kishi handled Sakura's maturity is absolutely astounding to me.
4). Bonds--- The friendship, parent, and teacher-student bonds are something I love to see. I like how focused this series is on friendship and relationships because those particular things have appealed to me for a long time. There are some exceptions over the bonds I hate, but I'm more or less content with the bonds message.
5). Development--- I'm most impressed by Sakura's, but the character development in Naruto is usually pretty solid and satisfying. Even if they don't always change for the best (ex. Sasuke, Hinata), you have a pretty well-detailed account of how they progressed to where they are now and how they started. Sasuke's fall to darkness, for example, was pretty good. It wasn't immediate and you saw what stages he went through until he reached the point of blind hatred towards Konoha (pre-War Arc anyway).
6). Deep meanings--- This manga/anime isn't a shallow one. It's just played for laughs and proving how strong you become. You have very deep messages of self-sacrifice, world wars, paths to leadership, and how you should treat those you love. My favorite will always be: "When you have someone to protect, that's when you become truly strong".
The Bad:
1). Asspulls--- The level of asspulls in this series, whether be a plot event or new jutsu, is ridiculous. I don't like asspulls in general because I always want things to be done in a satisfying manner and when something with no foreshadowing or logic happens, my interest turns into a big WTF. Some perfect examples I can think of is Naruto's insane amount of jutsu the moment he got the Nine-tails' Chakra mode (more specifically how he automatically knew what he had and how to use it), Itachi's Izanami, and Sasuke's annoying hax power-ups out of nowhere (Example ... hawk summon).
2). Sakura Neglect--- As satisfied as I am with her emotional development, I cannot say the same for her number of battles and her lack of plot involvement to degree Sasuke has with Naruto. Naruto and Sasuke are always the stars while Sakura is pushed back to the point some people see her a side character. I feel like, as Naruto's heroine, she have at least nearly equal involvement as Sasuke (who isn't even supposed to be the main character).
3). Team Taka--- I'm one of those few who still see no point to Team Taka. I love Suigetsu, but it's very obvious they will never be as important as Team 7 and don't see why they need to show up so much. To give Sasuke a team? Well, okay. But like I said: they aren't Team 7. You easily get rid of Team Taka now and it wouldn't affect the plot too much. They're just ... pointless.
4). Villain Treatment--- I'm tired of all of Naruto's villains converting to the good side. It's cool at first, but now it's seriously getting old. When you just feel like every villain will be "good", then they weren't really an engaging villain and they're harder to take seriously. If there was just one villain with no hope of redemption and just evil, then awesome. That'd be something new and way more interesting.
5). Neji's death --- Still disappointed with it's execution. Not only was it sudden and rushed, but it's basically condemning Neji to suffering the same fate as his father instead of changing the Hyuga cycle by changing the Clan. Maybe even becoming a head leader, a side branch member. That seemed a far more satisfactory end to Neji's character than that.
6). Tenten--- This character is literally there to take up panels. We know absolutely nothing about her except she fights with weapons and if Kishi's going to keep her around with Team Guy, then just gave her more character depth and personality. I swear, she is literally one of the most pointless characters in Naruto. What is there to her??
The Ugly:
1). Sasuke's Development Post-Kage Summit Arc: Just this. It irritates the hell out of me how Kishi has been handling Sasuke as of late. Nothing he does makes sense anymore. Sasuke deciding to "protect the village for Itachi" is still complete BS. I don't even hate Sasuke, but that came out of nowhere. I didn't like Evil Sasuke, but at least he was more consistent. Still obsessed with revenge, something that was supposed to be solved by Naruto. I still feel this would've turned out a lot better if Sasuke attacked the village and that was how Naruto vs. Sasuke would take place. All the foreshadowing had been supporting that so why? I don't know what Kishi was thinking when he decided to do that.
2). Karin: Out of all the Naruto characters, I'm pretty sure she's the one that got the worst. She's a character I can barely ever take seriously and her love for Sasuke is pathetic IMO. Her quick forgiveness after Sasuke tried to kill her was so degrading and embarrassing. Whatever Karin's background is, I would've thought her of all people would show more self-respect. That doesn't mean she couldn't still love him, but at least make him work for forgiveness.
3). Sakura's love for Sasuke--- This doesn't even need explaining. I've never been able to understand what it was about Sasuke that made her fall that hard for him, even when he was half-decent. He treated her pretty indifferently most of the time. Sakura didn't understand Sasuke. Sakura didn't interact meaningfully with him mutually. Sakura's love is baseless. And you always get flashbacks of her blushing at Sasuke, showing how shallow it looked. There wasn't a reason for such strong feelings and there still isn't.
4). Naruto's Sasuke Obsession--- I consider SN my brotp, but the way their relationship is shoved down our throats and overshadowed by practically every other relationship Naruto has irks me. He is literally obsessed with Sasuke to the point I sometimes feel like Naruto doesn't consider any of his other relationships just as important (from a writing-standpoint). Sasuke has down awful things to him recently, but somehow Naruto considers his bond with Sasuke more important than everything else. There's never a thought to Sakura or Shikamaru or Gaara nearly as much as it's always about Sasuke. Like I said, I like SasuNaru but not when it's at the expense of all Naruto's other bonds.
5). Hinata: As a non-Hinata hater, I would still say this is pretty self-explanatory. Hinata may be nice and sweet, but she has no substance but her love for Naruto. She has tunnel vision with nothing underneath. It's just "Naruto." It's not cute, it's detrimental to her character because there is nothing else to her. Shouldn't Hinata care more about being heiress than Naruto's acknowledgment? Apparently Hinata doesn't think so since she thinks of Naruto in practically every panel.
6). Reincarnation of Sage's Sons--- More recent, but equally as annoying. Naruto shouldn't have been written a reincarnation. All this "brothers, destiny, fighting" crap is ridiculous and heavily contradicts one of themes of the manga (Making your own destiny). Naruto wasn't supposed to be special. He was supposed to be a loser who excelled because of his hard-work, not because he was destined to start out a loser and then became a hero. It really takes away the meaning in his accomplishments.