Couple other things to clear up since you are incapable of waiting a few more stories to get all the information, lol (Talk about needing patience

).
-The married characters is actually something I was told I could do by members of this clan, Lei being one of them. I was told three years ago when writing my stories that the New Jedi Order, Luke's Order, allowed for Jedi to get married (Luke was married and the entire EU has to do with the byproducts of that marriage, his children) and as a RolePlay Clan set in the time during or after his reformation of the Jedi Order this was a permitted theme.
I think JO is a bit confused in some ways. It's set well after Luke's Order but somehow ignores his rules and the way he did things in order to prescribe to an older set of rules. At least, it seems so sometimes.
-I thought tying Mukhtar into the stories would help me tie things up as I move forward.
As stories go on it will be learned that Mukhtar heard of this prophecy from an Oracle, the Oracle feeds him information, Mukhtar uses it to do as he needs, in this case to draw out Vroxil. I have yet to decide what to do with the actual Oracle but the two are working together. Oracle makes the prophecies, Mukhtar acts as the face so anyone wishing to do harm to the Oracle will go after him.
-I edited the story slightly but the point remains. By the time Vroxil meets the 'Oracle' he's already exhausted, paranoid, and homesick. The whole story has him running around the galaxy on missions, he's always moving, fighting, and never home. He's worried Nexius is doing something behind his back but can't stay home to do anything about it, adding to the tension and stress. That's what the whole story builds up is Vroxil's fracturing which gives Mukhtar the opening he needs to break him. Mukhtar tells him what he needs to hear to break. He tells him everything his exhausted, paranoid mind has been thinking, feeding it.
-As for the Anakin ending, I couldn't avoid it in some ways as I started this story three-years ago but you are being a bit overly simplistic in your analysis. There are MAJOR differences here.
1) Anakin destroys the Jedi believing they are traitors to the Republic, Vroxil looks only to destroy a small group (the OF Council) of what he believes are Dark Jedi acting as Jedi. He believes the Jedi will call him a hero after this is over. Also, this gives the ground work for a later story where Vroxil does the exact same thing on Endor.
2) Anakin doesn't have a Jedi wife but he does end up killing her, Vroxil's wife is a Jedi and survives 16-years until he eventually kills her, but does so directly and not through a "broken heart"...
3) Anakin becomes a Sith Lord, Vroxil actually never does. In later stories it is revealed that Vroxil doesn't become Mukhtar's apprentice and instead leaves with Mikeman to train in solitude. This leads Mukhtar to try and recruit Christopher, the one he believes will have the most potential as he will be in his prime during the showdown (unlike Vroxil) and will have completed his training (unlike Mikeman).
4) Anakin loses, Vroxil doesn't.
I mean, sure, if all you look at is:
-Falls to the Dark Side
-Kills the Jedi
-Kills his wife
Then sure, but it's the small details that make the story. Also, the small details I haven't released yet. C'mon Mene, lol. It's like watching Episode 1 and Episode 6 and complaining too much is left unknown, lol. As more stories come, more answers will be given. Things that don't make sense here will make complete sense by the time the Chronicles are complete.
-Finally, the note to her son. The anagram, that makes an appearance in a much later story. Chris and YOU go to the OF temple so he can learn about his past. He's shown a computer console and it asks for a Name and Password, and Menelaos tells him what to put in. Menelaos knows what it means because Megan tells him. Megan tells him because Menelaos asked her to be in the Temple when Chris is there and the two of them talk in the Council Chambers before Vroxil interrupts... It all connects when the stories are done and read in order, I promise you.
I appreciate your comments though because it lets me know when I haven't explained some things right and when I have made mistakes in the logic of the story. It also helps me know when I'm doing the right thing making my readers go "wait, what?" so I can lead them to the "Oh, I get it now" three stories later, lol.