Filoni had to do a lot of work within the framework of the prequels which was hard.
You can say he ruined Grevious compared to how he was in the 2D show (where he was legit terrifying), but I'd argue that the General was already ruined by Revenge of the Sith and Filoni had to base him off of how he was portrayed in the film. And again, he had to work within the framework of the films and he could not have Grevious and Anakin interact with each other since they didn't meet face to face until the events of Revenge of the Sith, so that severely restricted what he could do with him.
As for Ashoka being a Mary Sue, I don't necessarily agree with that, though I can see how one can reach that conclusion based on how she was just inserted into the show despite no evidence of Anakin ever having a Padawan during this time. But I also think she was kind of necessary for the show to work because once she came on board, it was like "Okay, when and how does she die" and there was legitimate drama with her unlike all the OT characters who we know how they end up, and I actually quite like Ahsoka's development throughout the show from annoying kid sidekick to capable Jedi. And by the time you get to her confrontation with Vader in Rebels, I was fully invested.
As for other things Filoni did, he also gave us Cad Bane, the definitive version of Asaaj Ventress (not the Girl Maul version of the 2D show), and while the explanation for how Darth Maul survived is totally ridiculous, once you get passed that, the portrayal of Maul is actually really good. He also took piss poor aspects of the prequels (like Boba Fett being a 10 year old) and tried to make them work (like having 10 year old Boba try to get revenge on Mace Windu by hiding out on a clone training ship with other young recruits in training and planting bombs and shit all over the ship).
Filoni's show also presented Anakin in a way that was not insufferable. Again watch the 2D show and while the animation is great, I still want to punch Anakin right in the face. The 3D show at least got him to a point that was closer to how I envisioned Anakin, meaning he was capable, cocky, typically good natured, but also had a temper.
And hey I also liked the version of Thrawn we got in Rebels. Great voice, and had some great killer moments that captured the character I loved from Zahn's novels.
So yeah, I cut Filoni some slack.
That was the one about him getting his red arm right (MGS V for Droids)? Out of all the shitty new Disney content, the only ones I've genuinely enjoyed have been the Rogue One prequel novel, the Lando episode from Rebels (probably the only cameo episode that didn't come off as forced for ratings), the first Thrawn disney book which was a tie-in to Rebels (it was okay, and it had a sequel called Alliances which was pretty weak... but some gushed over it because "ThrawnxVader team up OMG"), the short-lived Obi-Wan and Anakin comics which were fun and had great art and The Phantom Limb which treated C-3PO with far more respect than TFA give him. I often see the Vader comics get "grand applause" from many, even EU fans, but aside from the first 3 issues, the charm fades away rather quickly, especially after they bring in Aphra, and even after she leaves the series just feels awkward and hollow at times.
Sadly, the whole red arm thing really amounts to nothing in the long term, despite Phantom Limb being one of the few non-fartyshitty stories under Disney since the red arm thing is quickly forgotten about and 3PO just gets a new gold one in following media.
Yes, that is the comic. To be honest, I was SUPER cynical about the red arm thing. Why does 3PO have a red arm? So Disney can sell new toys, duh! Can't sell toys of 3PO if he looks exactly the same as he did before, right? But at least they crafted a nice story around it that proved me wrong in the sense that I never thought 3PO could carry a story as a main character, but he did here and without mainstays like Luke, Han, Leia, Chewie, or his buddy R2 to lean on.
I agree about the Vader series. It starts off great and has some legitimately awesome material, but then sort of tapers off after awhile. It probably would have worked best as a 5 part miniseries. I kind of felt the same way about the main Star Wars book which started off killer, but then sort of meandered around and I stopped reading after issue 10 or so.
I like the Thrawn books Disney has released, mainly because it is just great to have Zahn writing him again. The Vader/Thrawn book was good mainly because the moments where Vader and Thrawn interact are great...I just wish the main story was something a bit more juicy.