The dragon experiment was a set-up.
Specifically, rebel agents sabotaged it in order to get a shot at the wizards' top brass. Roheis and the other conspirators note later on how fortunate it was that so many of the most senior wizards (and the ones most relatively loyal to the king) disappeared in one fell stroke: This will make it that much harder for them to act decisively when the coup is launched. Perhaps it was more than just good fortune behind it.The "witch" spoken of in A Sea of Skulls is a fourth Watcher
Or possibly the female Watcher already revealed, but then the pieces don't seem to fit together. Nothing earlier on suggested that she was involved with the Horde, and indeed her heavy involvement elsewhere hints against it.Marcus will return to his theological studies after the war
It's clear that he doesn't really like the military, even if he's doing a good enough job as an officer so far. Then add the trauma of the civil war to that. Once the war is over, he'll be very happy to get out. This assuming, of course, that there is a Happy Ending for him....Marcus will marry Caitlys in the end
She will learn from Bessarias, realize that magic is evil and give it up, and convert to the Amorran religion. Thus, there will be no obstacles to them marrying (except the setting's massive Fantastic Racism, obviously, but that sort of thing rarely stops the romantic protagonists in this sort of story). Possibly, Bereth will play some part in this as a Deliberately Bad Example—specifically, the career girl who does not marry and ends up lonely and unhappy—given how the second book seems to be setting her up as a foil to Caitlys.Amitlya will reappear in the main series
Out of the archmages who appeared in the prequels, she is among the few who are mentioned in A Throne of Bones, and the one who is given by far the most attention in that conversation. Given that the elves begin to play a larger role again in A Sea of Skulls, and seem as though they may soon need to call up their remaining Person of Mass Destruction (after Bessarias became a magical pacifist), this looks a lot like Foreshadowing.The Amorran God isn't actually anti-magic...
...He just made this a part of his doctrine to make Amorr a strong Anti-Magical Faction, who can function well without wizards. Given that mages aren't very effective against the Watchers, but on the contrary easy bait for their Mind Rape powers, this was probably a good way to prepare Amorr for the war that seems to be coming now that the ancient horrors are beginning to crawl out of the woodwork.