This can be a broad topic of alternate EU ideas, but first off, I'd like to explore the idea of "What if Anakin lived and Jacen died?"
First off, Jacen died while trying to kill the Voxyn Queen, becoming one with the Force in an awesome display of combat, fighting side by side with Anakin. The battle seen would be very similar to the book, but in this case both Anakin and Jacen are fighting the last stand for double awesomeness, yet Jacen dies and Anakin is captured by Vergere.
Now here's where the fun begins
If I were to rewrite the EU for this alternate reality spin off, Anakin would not have put up with Vergere's torture lessons, and would have killed her and made a narrow escape from the seedship. I would have altered scene when Jacen was killing the dhuryams, in this case it would be Anakin, but instead of stopping on the last one, he would have stabbed through Vergere and killed it...but he would have escaped before the ship collapsed on itself and died.
With Vergere dead and the Vong's hope for a new homeworld gone, Anakin has struck a major blow toward the enemy. He'd go on to win more battles, have the big stand off with Shimrra and Onimi.
Again there would be another folcal point. With the Vong's leader dead, the warrior caste would recognize Anakin as their new leader, submitting to his obvious favor with the gods and his superior combat skills and powers. Anakin would give the Vong the planet Ithor, putting them in charge of vongforming it so they could have it.
I would somehow do a new spin for Dark Nest in which Anakin goes out to find and rescue Raynar. I would also make it that Raynar doesn't get all messed up in the fire from his crash.
Then there's the big question of Legacy of the Force. The obvious spin would be to have Anakin now become Darth Caedus, but I'd rather see Jaina take on that role. To add more spin to it, I'd actually have Anakin consider joining her and becoming her apprentice or co-ruler. However he'd come to his senses, and would ultimately redeem her.
Fate of the Jedi would then have Anakin and Ben facing off against Abeloth while Luke deals with the Daala and her regime.
Course that's an overly Mary Suish alternate timeline. But it is fun to play with the idea.