1. The fact that Krayt rules with an iron fist and nobody dares challenge him ever since he created the order, which is basically contradictory to the way of the sith.
1. He changed the Sith, and he's called on it in the comic by Bane, and Anneudu they no longer go by the standards of treachery and betrayal, its not the first time its happened ex: Exar Kun and the Brotherhood of the Sith, if anything Krayt is following the Sith ways of the one TRUE Dark Lord Exar Kun who was appointed by Ragnos himself and order was legitimized. If we wanna really play this silly little game of "legitimacy" then Bane the one who throws a hissy fit at Krayt is the true heretic.
2. Are you not reading Legacy? Cade says in the latest issue that the Sith ARE infact plotting against Krayt, and a few issues before that it SHOWS Maladi and Nihl complaining about Krayts rule. There is very much treachery in the ranks.
No Plot Hole.
2. The outcome of the Skywalker/Solo clan. Since the Legacy authors rushed the dates, it has been almost 100 years since the end of Invincible. So what happens to the clan?
You do know Legacy the comic was planned WELL before LOTF the novels and Del Ray was originally going to have the LOTF series be set in the New Sith Wars era. Its Del Ray's fault NOT Dark Horses.
And jesus the comic series is only 25 issues in, have you ever heard of a thing called mystery? Moreover the fate of the Solo clan right now isn't relative to the plot. We already know the fate of the Skywalkers: Nat, Cade and Kol. As the author John Ostrander has said these plots will be revealed in time, when Del Ray either starts directly tieing into Legacy (as they are starting to do now: The One Sith appearing, Jagged Fel being made High Moff etc) or Del Ray stops doing novels in the Legacy era (They won't) so quite frankly: be patient.
Still not a plot hole, a plot MYSTERY it is though.
3. Krayt apparently learns from Xoxaan's holocron for more than 10 years? What does he do the next 10? Sit in the embrace of pain?
Once again not a plot hole were TOLD what happens, even though its pretty obvious he studies the holo, leaves Korriban to fight Vader and Palpatine, sees there dead, runs to the unknown reigons in an emo fit, gets caught by the Vong, has Vereger shape his value system, escapes Vong, goes back to Korriban to found the One Sith.
4. The fact that the power Plagueis and Palpatine have searched for their entire lives comes naturally to Cade Skywalker
OMG a SKYWALKER is unnaturally powerful, and has a talent never seen before this has never happened...Oh Wait...it does...with EVERY new generation of Skywalker. Really, thats just a complaint on your part AT BEST.
5. The sith order being more powerful than the Alliance and the Empire right now.
There are many more and I will list them when I remember.
Please do because so far you've shown me ZERO.