The only titles I've watched that I enjoyed more are Gankutsuou, Steins;Gate, Hyouka, and Usagi Drop (If you want to be horrified, you can check my MAL to see all the anime I've watched). Certainly I don't mean to say that only those four surpass Naruto in quality; however, no others were for me as enrapturing and stimulating.
That's odd. I have no problem saying that Gankutsuou, Steins; Gate, Hyouka, and Usagi Drop surpass Naruto in quality.
Big Guy laid out a lot of the pitfalls of Naruto, which are mostly genre based, but not all shounen battle anime that follow the typical tropes suck balls. Just off the top of my head, Index / Railgun, Hunter x Hunter, Magi, and Soul Eater manage to either avoid or embrace said tropes in unique ways. Some, like Medaka Box, end up being parodies and deconstructions while still working as actual shounen battle manga. This isn't to say that each doesn't also have weaknesses, but there are certainly mold breakers and then there are not. Inevitably, what really kills a shounen battle anime / manga is the length. Popular manga / anime keep going well past their expiration dates. The most widely known example of this is Dragon Ball, which was supposed to end a couple of times, but was pushed forward by publishers who still wanted to milk the cow (even going so far as to punt the original creator's wishes and carry on without him). Length has really hurt several manga over the years, which has resulted in mass continuity inconsistencies and / or outright handwaving. Bleach, especially, is a victim of this. One of the few popular battle anime that has managed to avoid a lot of pitfalls is supposedly One Piece, but I haven't seen any of it so I cannot comment.
So a lot of negativity comes from that, but there is enough obnoxiousness from Naruto itself that rustles jimmies. I'm not as familiar with the show as others, but I know a lot of the characters are either very poorly developed and one dimensional or just outright hated by the fanbase. Naruto himself has his fans and his foes, but I don't think anybody gets it quite as much as Sakura. Part of that is the failing of the writing itself, as she is treated like another common shounen battle manga trope: a wimp who often ends up the damsel in distress or helpless bystander more than an actual beneficial member of the "nakama". Female characters in battle manga tend to be this way, especially the "lead" female. Give me a battle manga, and I can point out that character easily enough. This is just an example I've gleamed from comments, so don't take it as my own personal critique.
Another blot of negativity is from the absolutely horrifyingly bad filler episodes that carried on way too long. One website notes that both Naruto and Shippouden have had roughly 40% of their existing episodes as filler. That's way too high a number. I realize that anime often catch up to manga, but I am so anti-filler it isn't funny. I would rather they cut the show for a later season or air re-runs for a year until the new episodes come out than do filler. Having not experienced the pain of the year long Naruto filler arcs, I can't comment as to how much it would have aggravated me, but having experienced something similar with Bleach (which I did watch), I imagine it would have pissed me right the **** off.
I'm sure there are other issues. I know a lot of negatives were waned when Shippouden came out, but it seems that lately some of those same gripes are starting to return. Like I said, nothing kills a show like not knowing when to quit.
Lastly, I would say that whatever attachment you have to a series is based on nostalgia or, by your admission, familiarity. It is the first anime you watched / enjoyed, ergo it will always mean something to you than anybody else. I personally have the same irrational attachment to Macross, but that shouldn't stop you from being able to make an honest assessment of what you're watching. Enjoyment is one thing, and an important thing to an anime's value, but it isn't the only thing. I mean, you could enjoy MD Geist all you want, it's still a shit anime.