There are basically three segments of Hunter x Hunter.
The first segment is everything from the start until when they meet Kite. This segment is mostly about training to get stronger and solving puzzles through clever thinking. It's a very simple story with very shallow characterization. Occasionally there's an emotional moment where Killua shows how much he values his friendship with Gon, but that's like a once every 20 episodes thing, whereas 'lets train and get stronger' is every single episode.
This first section of the story is harmless but also uninspired. It just feels like a generic shonen action story with no one you can really identify with or get behind. The number of times the enemy keeps sparing our heroes gets pretty retarded too. The fights are always low stakes and easy as a result.
Hunter x Hunter would be worse than Kenichi or Flame of Recca if it stayed like this. However, upon meeting Kite the story takes on a totally different tone.
In this second section of Hunter x Hunter, everything becomes serious and intense. Heroes start losing fights that matter and not being spared, but just plain dying. Gon and Killua go through actual trauma they find hard to rebound from. Millions of innocent lives are on the line and there's no room for error or playing around like that silly Greed Island arc. Kite is the first badass hunter we meet -- everyone before then is weak-willed or weaker than Gon and Killua, leaving a bad impression overall for the entire organization. Then we meet Morel and Knov, and it turns out there are some competent hunters out there after all. There's lots of emotionally rewarding content in this segment, which goes all the way until Neferpitou begs Gon to let her heal Komugi and Gon agrees after getting in a fight with Killua over it. This is the climax of the series in terms of quality. There's actual drama, actual complicated relationships, genuinely empathetic bad guys, the story sings. At this point you're thinking, Hunter x Hunter is the best shonen action story ever! You feel like promoting it to 30th, or 10th place. The sky feels like the limit.
But then you suddenly enter the third phase of Hunter x Hunter. This is the only way I can explain it. The chimera ant arc becomes unhinged, and a series of ridiculous deus ex machinas start piling up one after the other consecutively favoring the heroes. The storytelling becomes awful, the pacing becomes awful, and the writer even takes several episodes off to just moralize and not even talk about the characters and the plot at all. Multiple episodes are written about the adventures of an octopus on a fruitless journey to find the elusive Palm. There is absolutely no reason for these episodes. They're extremely boring, they're in the middle of the intense fight between Netero and Mereum and Gon and Pitou, and they end in a meaningless way that has no impact on the rest of the story. Likewise, the fight between Knuckle and Youpi, after seemingly dozens of episodes, just fades away into a meaningless tie as they both go happily along their own way. This is stupid. All that hype was for nothing. Netero's fight with Mereum was for nothing because he could have just set off his killer bomb at any time from the start. It was just a bunch of wasted motion, a waste of our time. The King getting healed and threatening our heroes once more was a waste of time because he was already poisoned, so the 'suspense' the plot was delivering was all fake.
And then there was the mother of all ass pulls, Killua having another brother (never mentioned before now) who literally has the power to grant wishes. Any wish, no cost, Nanika can just do whatever you tell her to do for free as often as you want. Tons of episodes are wasted describing all the limitations this wish granting genie has, only to be revealed at the end that none of these rules apply to Killua who can just have infinite wishes for free whenever he wants. This is the worst writing I've ever seen. If wishes could be granted from the start, why didn't Killua use wishes to defeat the Chimera Ants? Or escape the Zoldyck home? Or any other time he was in a pinch? Furthermore, what kind of terrible story says problems can be solved by making wishes instead of hard work? In the real world, it's impossible to get a meaningful reward without putting effort into it. Stories need to reflect that fundamental truth. There are no shortcuts to Hokage, was one of the first things Naruto told Konohamaru in Naruto. Naruto had to work to become Hokage, and you could tell how much he sacrificed for his dream, such that you felt happy for him when he finally achieved it. But wish granting? That's just bullshit. This cheater just cut in line and got his reward without any effort at all. People like that aren't sympathized with as inspirational heroes, they're despised as meaningless frauds.
Any good will Hunter x Hunter developed during phase 2 is pissed away in phase 3 by talking koalas who meander about the philosophy of reincarnation and meaningless elections which have no relation to any of the main characters. It's some of the worst writing ever published, and you can tell that the author is totally out of good ideas and was just flailing around with whatever crap he could come up with before ultimately giving up and quitting, which is why the series still has no ending to this day. Kurapicka still hasn't captured the spiders and so the entire York Shin arc was a waste of time. No rematch between Hisoka and Gon, just another thread left hanging forever. But don't worry, you get to hear all about Koala-man's life. Oh, and that emotional moment where Kite dies at the beginning of the Chimera Ant arc? Never mind, he's brought back to life, no worse for wear, don't worry about it. Because death isn't permanent so it's not sad. I learn so many things from Hunter x Hunter. If you want something you have to wish for it. If someone dies don't worry he'll just become a cute girl friend in a few weeks with all memories intact. If your fifty episode crusade to take down a last boss fails, then just use a cheap grenade consumable you can buy at the corner store and you'll auto-win. Why didn't I think of using that against Sephiroth in FF7? Then I wouldn't have had to level my characters at all. . .
The third segment of Hunter x Hunter is so bad it erases all good will that was generated during the second segment. I simply loathe the last 25 or so episodes of Hunter x Hunter. Which leaves you basically where you started, with the first segment, of a decent action adventure shonen story not very different from Kenichi or Flame of Recca in execution. I thought about changing my 98th ranking for Hunter x Hunter all the time while watching, but now that I've gotten through the whole thing it's about right. I can't totally hate it because I have fond memories of part 2. I can't like it because part 3 is unforgivable. So halfway inbetween is the best I can do.
However, for a show with so many episodes to work with, 98th is a pretty abysmal showing. There aren't any shows with more episodes than Hunter x Hunter ranked lower than Hunter x Hunter (though Macross gets close.) But when you have 146 episodes to work with, it's not difficult to beat 6 episode oav's or 12 episode introductory teaser seasons of other shows. Just one or two good moments and you've matched all Alien 9 can possibly provide. Hunter x Hunter is a great anime, better than 77 other great anime, but with the number of episodes it had to work with, that's not nearly as commendable as it seems. Ojamajo Doremi is the next lowest series with a comparable length to Hunter x Hunter, and it's at 41st place, and that only because it had an equally awful ending as Hunter x Hunter's. The next lowest rank of a long series is Inuyasha at 31st. Normally speaking, an anime with 146 episodes should be at least in the 30 to 40 range, then. And yet here it is at 98. Which makes it share the worst 'per episode quality' series in my rankings with Macross (home of the endless Macross 7 which should have been shrunk down to 12 episodes or so but instead went on for 60. . .god help us. . .)