The fact that Aeon is listed a villager in Order of Ecclesia is huge and makes me run wild with speculations.
First, if Aeon really is a villager rather than a guest to the timeline, he would probably be the town watch maker. Even if he is posing as a villager, he's probably disguised as a watch maker. You'll probably have some watch related task. Maybe the task that you do for him will actually give him his powers over time?
Second, this makes me wonder if perhaps the native time period for the game Judgment is right after the events of Order of Ecclesia. Is OoE a prequel to Judgment? So perhaps Shanoa and Aeon are the only characters in Judgment who are not "out of time".
Third, I've heard in a few reviews that the main villain of OoE is not Dracula. Who that real villain is is suspect and the "heirarchy" of villains is unclear at this stage of the game. Is it Barlowe? Is it Albus? Maybe we'll find out that the one pulling all the strings in OoE is Aeon. We have no idea what his motivation for any of this is. Is he trying to alter the events of 19th Century? (perhaps wiping out Nathan Graves's and Cornell's quests from the timeline in the process or creating a divergent timeline for them??)
Fourth, if Judgment is really this tied together with Order of Ecclesia, we might have to conclude that Judgment really is a canonical game. This could easily be the case if most character's memory is wiped out at the end or if in the end, time get's set back on track as if it never happenned. But that would surely mean that any of the background stories developed for the characters and the characters' "character" can be considered canon, and a lot of things might be explained along the way.
We'll see.