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 and isn't confirmed to be bisexual.
There's also a lot of pretty blatant Belligerent Sexual Tension between Kusanagi and Kurutsu, but this still doesn't stop the detractors.
In terms of the final product, there are a few different camps of opinion. One camp considers Arise as an inferior adaptation of the GITS franchise. This is largely due to lacking the focus on philosophy and existentialism that's been there from the beginning as an important part of the franchise. Another camp finds it that they don't mind the flaws and enjoy it because it captures the essence of the franchise despite lacking the philosophical content, which they see as pretentious (particularly in Innocence). The third camp sees it as So Okay, It's Average and not really as memorable as other adaptations.
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.
Some viewers can't help but find Motoko's facial expressions very hilarious and cringe-worthy. Of course, they're probably used to SAC!Motoko's character design.
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.