There's certainly a lot to look into in order to fix it. I'd start by addressing exactly how "divine" ki works with the Saiyans. Base Goku (RF) should be > SSG Goku from BoG, which is only really implied and never stated. This would make determining quite a few character's power placement a lot more straightforward -- like Cabba -- and gives us a better way to determine transformations and such.
From there I would move on to Hit, drop Goku's Kaio-Ken and let it play out like the manga. We are presented with a fairly reasonable chain of power in the manga, something like: SS Blue Goku ~ SS Blue Vegeta >~ Hit (Full Power) > SSG Goku > Base Hit >~ SS Goku ~ 10% SS Blue Vegeta. I did think Vegeta being at 10% was kind of lame, but its easy to make this work.
It starts to get shitty when we bring Future Trunks and Black into this, Trunks makes the statement that Black >~ SS3 Goku. We then watch SS2 Goku fight Black, and Goku seems to have the advantage if anything. Pyro, we had a discussion about this recently and for now, I'll still go with Black allowing Goku to beat him so Black could become stronger. The biggest issue with all of this is Trunks going from having trouble with Dabra to fighting guys like Black or SS2 & 3 Goku, who should all be superior to SSG Goku from BoG. I would either drive Trunks' power way down, or have him do a lot more training -- probably the RoSaT -- and not have the only reason for him being so strong that 3 minute session with Vegeta. When the guys go Back To The Future, I'd make it clear that SSB Vegeta & Goku > Base Black who had gotten stronger and that Super Saiyan Rose Black >~ SSB Vegeta & Goku. I don't really know how I'd go about Trunks' new tranformation, its ridiculous. With Merged Zamasu I would just have him annihilate the trio and force the fusion into Vegetto much quicker and have Vegetto win.
Fuck Shisami, Tagoma and the 1,000 soldiers. I'd just write all of them out.
I'm too drunk to put any more into this. also suck my balls for calling us neckbeards.