I actually agree with a lot of this. First, I really liked Revan, when he was how we interpreted him, and how he was a "legend of his time". That said, I hate that he is in TOR. It really did kill Revan for me and a lot of others, spawning the Revan haters we have today. While I am glad we have a book explaining what happened to him after KotOR I'm not exactly in agreement with how he was portrayed. Personally, I think the book should have been about his fall, and somehow explain differently how he prevented the Emperor from attacking for 300 years.
As far as the Cults go, YES to more Darth Nox cult missions.
The thing about Vitiate and Marka Ragnos, I think it would be cool if instead of the Jedi killing Vitiate, the Sith did it themselves, either Darth Nox, Darth Marr, or even the spirit of Marka Ragnos or Tulak Hord would make for an interesting ending, going along with the lore that Sith destroy each other. Ironically, Nox is now more immortal than Vitiate, so how the hell does that work? And how does/will Nox ever die?
Quite honestly, whatever explanation for Vitiate not attacking they could give (both the one that was effectively given, and the ones they could/should have given) would not be believable, because the KotOR plot has so many loopholes. Regardless of Revan, Vitiate should have attacked during the events of KotOR 2, when the Republic was in disarray and there was no Jedi Order to protect it. The reason he did not is a mystery, a stretch and a majour loophole. So that situation really could not be salvaged in a believable manner.
But on the case of Sith destroying Sith, I would oppose that spelling doom for Vitiate and his empire, seeing as that is what ends the New Sith, and that pertains to the prophecy of the Sith'ari, the Dark Lord that would rise, destroy and recreate the Sith in his own fashion. Darth Bane fills that role, so he's got the dibs on that approach. I would much rather see the relationship with Vitiate's Empire and the true Old Sith Empire developped, crippling the Sith Empire, but its final end should come at the hands of the Jedi. It would be a nice closing, too, since all the other wars in the Old Sith Wars were ended by the deeds of the Jedi.