So now that it's the end, I wanted to see if I could go back and try to edit this series in a way that makes it better. I tried to keep to the rule that I would cut nothing entirely so as to keep to Kubo's outline. Arc by arc, this is what I'd do:
Substitute Shinigami Arc is great, I wouldn't change a thing. Good set-up for characters.
SS Arc: I'd start by axing like 4 squads. Komamura, Gin, Tousen, and Hitsugaya are no longer captains. I'd completely delete Komamura, Gin, and Tousen. Koma does nothing except bitch at Tousen, and Tousen does nothing either, so cut that out. Gin is wasted as well, so ax him too. (Note: whenever I cut minority characters, I'd try to replace them elsewhere). Hitsugaya gets moved to Yamamoto's lieutenant instead of Sasakibe (who also did nothing). This lets him keep his "probably going to be head captain someday" schtick in a way that makes more sense. He also never feels strong enough to be a captain. You also don't need more than 1 traitor to get the point across, so Gin and Tousen are superfluous. Just let Aizen do it. By cutting this down, you get less characters to deal with unresolved powers later. And I think 9 is still enough numerology for Kubo's thing.
Hueco Mundo/Fake Karakura: First, there are no Vizards as a group. I love them, but they do nothing as a whole, so I'd just create Shinji, who shows up and trains Ichigo in his Hollow powers. You still get the "Aizen betrayed me and got me kicked out and I have a mask etc..." stuff, but with less fluff characters. I'd change Ichigo's power level to match Ulquiorra's instead of Grimmjow's. Then Ichigo pretty well handles Grimmjow, so you still get Grimmjow's "Damnit I'm not strong enough" thing. The main reason I'm buffing Ichigo is to indirectly buff his human friends. At no point should anyone from the Squads (other than Rukia and Renji) show up in Hueco Mundo. Renji and Uryu should be able to beat Szayelapporo, and I'd give Chad a good fight with Nnoitra. I'd make all of the Espada stronger so as to require Captains to work with their lieutenants to defeat each one. I'd make it so that most bankais are revealed here, including Yamamoto, Kyouraku, Ukitake (whatever it is), and Shinji (whatever it is). Add in bankais from Kira and Hisagi too if you want them to have those at all. Aizen ends up saving his and proceeds as normal. He beats Yamamoto without his cheap trick (establishing more power for himself), and then gets beaten by Ichigo. Done.
Fullbringers: I'd scrap Tsukishima or tweak him in a way that makes it so that he can't take out Ichigo's human friends. Then I'd stretch this arc out a bit to allow for longer fights at the end. Like Hueco Mundo, the Shinigami should not bail out Ichigo here. This should be the final showcase for the humans. Let Chad, Uryu, Orihime do some work here, and maybe toss in some of Ichigo's school friends. When it's all over, kill the bad Fullbringers (so they don't show up later), and I'd do something so that Ginjou's old badge goes over to Karin, who can then become the Shinigami dealing with minor Hollows in Karakura Town. This wraps up that thread. I know a lot of folks would probably cut this arc, but again, I'm trying to outright cut as little as possible. I think this does a good job of helping out the humans with their screentime and deals with several lose ends. Also, name Ichigo's damn Fullbring!
Quincy War: Cut out all of them but 4 Sternritters and Yhwach. Since we took care of most bankais earlier (this is why!), we can leave most Captains out of this. Let the Royal Guard do more against the 4 Sternritters. Change Yhwach's story from a stupid "It was always me" thing into a war survivor from the past genocide out for blood. These 5 (plus Uryu and Ryuken) are legit the last Quincies. No bankai theft ever happens. Yama gets beaten in a more fitting manner, and replaced by Unohana (who then reveals her past) instead of Kyouraku. I like that Ichigo is actually a Quincy, so keep that, but Yhwach doesn't know it (e.g. Ichigo almost dies, but activates Blut Vene accidentally, which surprises everyone but Isshin). Aizen needs bankai (whatever it is) to help beat Yhwach. Proceed to epilogue as you were.
General changes: Mainly, Ichigo's moveset should grow. He's already got like 4 bloodlines in him, so keep that and use it to improve his fights. He should use Cero waaaaaay sooner than against freaking Yhwach, and honestly, I'd make it so that he works arrows in there as well (for instance, take that chain on the back of his true bankai that he has now and make it a bow string. He can then use the giant blade as a bow as well). Let his Fullbring do more (since it was his most interesting power. I'll remind everyone that it wasn't a straight fighting thing; his Fullbring was the power to bring inner power out, so play with that wording!). Also, pace the fights better.
I'd love some comments on things, but I think this would salvage Kubo's work without cutting too much of it.