Legacy of the Force was the result of a huge Xanatos Gambit by Abeloth.The Jacen plot is not a red herring. Abeloth was the main Chessmaster behind his fall from grace...she just didn't do it directly. Somehow she managed to get Lumiya under her control; Lumiya was flying under the Alliance's radar for quite a while, so it's not inconceivable that she could have ended up in the Maw somehow. Then, she sent Lumiya to turn Jacen to the Dark Side; she might have even fabricated the "Tassels" which were telling Jacen to sacrifice someone he loved. As we all know, this resulted in the death of two of Luke's biggest love interests, Mara and Lumiya. Once that was done, all she had to do was kill Akanah, and Abeloth would have Luke all to herself. So...yeah. That whole book series happened because some Eldritch Abomination got lonely and jealous. Still somewhat lame, but it makes sense.
Daala has been driven crazy by Force Psychosis.She's not a Jedi, but she did spend a lot of time in the Maw. And since she wasn't a Jedi, she wouldn't be able to defend herself telepathically, like Ben just barely managed to be able to do. It would certainly explain why she seems to be so needlessly paranoid at times...
Jaina, after marrying Jag, will leave the Jedi Order and found the Imperial KnightsSeeing how the story's going right now, it seems like the most legitimate explanation for the Force-sensitive Fel Dynasty and its Force-wielding Praetorian Guard.
The dark figure Jacen saw ruling the galaxy in his vision was himHe saw a vision of someone ruling the galaxy and foolishly assumed he could prevent it by... ruling the galaxy. Thus turning it into a case of Self-Fulfilling Prophecy. When Luke and Ben see Allana ruling more benevolently, it's not because Jacen's changed anything- they're just seeing a later future than he did.