These are what we call the 'YMMV items.' Things that some people find in this work. We call them 'your mileage might vary' because not everyone sees these things in the same way. This starts discussions in the trope lists, a thing we don't want. Please use the discussion page if you'd like to discuss any of these items.
The character designs have been changed many times as pointed out in this article, but the new character designs still caught a lot of flak, especially Motoko's which could easily be mistaken for a teenager.
For some, the new voice cast unlike the Oshii movies and the SAC series where they retained the original cast.
Several people were upset that Motoko's dating a guy instead of being bisexual.
Which is kinda odd, because being bisexual explicitly means being active on both sides of the fence, including (gasp!) heterosexual relationships. Unless those offended interpreted the term "bisexual" as "lesbian, but without saying so", of course.
The story itself where some viewers complained that Arise doesn't tackle the themes (along with the Techno Babble and philosophical discussions which is a staple to the franchise) that the franchise has been dealing with and it has become an ordinary cop drama. Others cited that the occasional Techno Babble is notoriously pretentious which the second Ghost in the Shell film suffered from.
Genius Bonus: Motoko's mention of Saito's old JGSDF job as a Marine. While the actual JSDF doesn't have one, the Ministry of Defense has made recommendations that the force should have a marine/naval infantry force to conduct amphibious assault in a future conflict if any of its islands or outlying territories are captured by enemy forces due to tensions with China over the Senkaku Islands.
Actually, JGSDF's Western Army Infantry Regiment is essentially a Marine regiment right now, but they're technically Rangers. Which, to think of, kinda meshes really neat with Batou being an ex-Navy officer in Arise, while keeping his canonical Ranger qualification.
The closest thing possible is the Special Boarding Unit, which is the JMSDF's version of Navy SEALs.
Narm: Motoko's face while using a chokehold on one of the cyborgs.
Tainted by the Preview: The different art style and character redesigns turned off a lot of fans from watching the series.
Tough Act to Follow: The music itself done by Cornelius, who also did Appleseed: Ex Machina soundtrack. While soundtracks of the Oshii movies and Stand Alone Complex series are done by renowned composers, Kenji Kawaii and Yoko Kanno, respectively, the Arise soundtrack didn't really live it up.