Oh man, I have a lot of opinions on this job. I think there are a lot of reasons it's always been one of the least popular jobs, even prior to its 6.0 undertuning + Raiju issues.
  • The skill floor/ceiling: Basically, the job is too intimidating to learn to appeal to a lot of newcomers/casuals and too braindead once you've learned it to appeal to a lot of challenge-seekers/optimizers. Even if you just want dat high APM, the 45s of almost nothing but 1-2-3 makes the job a hard sell.

  • Gear: it's currently the only job that doesn't share armor with any other job. This makes it inherently less appealing if you intend to raid since you're effectively locked into a single job without putting in 2x the effort to gear up. Every other job has at least one other option that just requires a different weapon. Sharing accessories with p. ranged isn't necessarily a bad thing, but unless you can find a flexible static with another person willing to alternate between melee and p. ranged, you'll need to get a whole other set of accessories.

  • Rogue requires you to go rather out of your way to unlock, starts at level 1, and is absolute dogsh*t to play. It has to be most miserable 30 level to get through in the game and it somehow keeps getting worse every expansion as more and more of NIN's assassin/rogue skills get removed to make room for Naruto stuff. The thematic gap between Rogue and Ninja is much larger then it is with any other ARR class/job, which makes it really difficult give you anything interesting to do earlier on, like they did with MNK in EW. This thematic gap also turns off a lot of people who were more interested in the rogue job fantasy, while SAM, a job that starts out at level 50 with a bunch of awesome skills, syphons away a fair number of weebs.

  • Trick Attack just isn't very satisfying to use: I know the debuff is supposed to primarily benefit the party, but it just feels like such a miniscule personal gain. Also, NIN's burst doesn't really feel that unique anymore now that every DPS has at least 1 crazy burst window every 120s. Honestly, aside from the initial Hyosho Ranryu/DWAD, it mostly just feels like generic filler at this point. SAM or RPR's burst feel way more unique and impactful.

  • Finally, its a minor thing, but I really dislike NIN's pre-pull setup. Every other DPS can pretty much hit the ground running now, but with NIN you still have to do the clunky Huton, Hide, Death Blossom, Death Blossom again because you used it too early song and dance. Seriously, what's even the point of Hidden decreasing your movement speed? Would it really be that OP if you could move normally while affected by that completely useless status?