IMO I do not see how you can go into a season 3 where Root A ends. I am a fan of root A despite its flaws. I know Ishida-sensei had a vision for his what if story but sadly it got cut up by the studio resulting in the messy but somewhat poignant s2.
However due to certain elements of season 2 the transition to season 3, which I would assume would adapt Tokyo Ghoul: Re would be nigh impossible without retconning a majority of s2 out of existance. There are certain events that must take place, certain characters must interact and not die as well as other highly manga spoiler territory issues that must happen.
However I will highly agree that ghouls biggest flaw was that it was not treated like the senin it is. The anime, while I adore it, did take out a lot of quite and impactful moments that were more psychological and though provoking. I also agree that Touka' s character did get downgraded from the complex character she is in the manga but it pales in comparison in how Tsukiyama was neutered to become a gag character.