The Duke has banned Pawns from entering his castle, presumably simply because they are not human. Might it not instead be that he is afraid his old Pawn will recognize him, or that another Pawn will somehow know that he did not defeat the dragon at all?
Just before the begining of the final battle, Aldous informs you that the Duke has selected you for a Super Special Mission that's very dangerous and involves being sent far away for a long time. Of course he has, and not because it's a 'great honour'. He's done it because you've seen him in the throes of madness, trying to strangle (or, depending on how you completed the quest, outright murdering) his current wife while lamenting causing the death of his previous beloved. Plus, he may think his wife's cheating on him with you. And, as a bonus, it might occur to him that if you manage to defeat the dragon, bad things might happen to him (as he's still bound to it) and word might get out about the deal he made; meanwhile, if you choose the deal yourself, you might usurp him. Basically, the whole thing is a blatant Uriah Gambit.
Except the Duke's attempted murder of his wife takes place in a missable/skippable side quest. At no point do you actually have to complete (or accept, or even discover the existence of) "Arousing Suspicion". The other reasons for him wanting the Arisen gone are still logical, though.
Whether or not you've participated in the quest and seen it, the Duke kills his wife if you do not intervene. If you don't talk to her in your one chance after 'Come to Court', she vanishes from the game entirely.
Going by its name alone, the "wyrm hunt" campaign is supposedly intended to bring arms against the Dragon. Except every single quest in the campaign has involves everything but hunting down the Dragon - uncovering ancient artifacts, translating old texts, investigating a cult, and reclaiming a fortress siezed by Goblins. Meanwhile, characters like Julien lament the stagnant state of the kingdom, sitting on its thumbs instead of taking any real action against the threat of the Dragon. When you learn the Duke's history, it suddenly becomes very clear that this is all by his design - better preoccupy your kingdom and guardsmen with distractions rather than endanger the life of the creature whose survival maintains your immortality.
Whenever you kill a Drake in the game, they utter the phrase "the seat of God lies beyond". It could just be a cool line, said because they're dying and about to go to the afterlife. Or it could be a reference to the end of the game, with the Seneschal's throne as "the seat of God".
The Cyclops has very elephant-like features. This is noteworthy because it's believed that elephant skeletons were the inspiration for the Cyclops myth. Nice little touch there, Capcom.
All dragon-type enemies can possess Pawns, and that ability isn't just to make them tougher opponents to fight. It's a hint that dragons are created from Arisen (your Arisen can potentially become the next Dragon, and the official artbook states that the lesser dragons were created from Arisen), and given that Pawns serve the Arisen, it makes sense that the dragons are able to exert some form of control over Pawns.
The player Arisen will grow extremely powerful over the course of the game and the story. One of the most devastating powers the Arisen is able to do is all done within the Sorcerer class. They can create giant tornadoes or creating devastating earthquakes to stagger even the most powerful foes. It's strange to think how a normal fisherperson was able to go learn and accomplish this...until the Seneschal's reveal. Arisens weren't only chosen by the Dragon to come try kill it, but are also candidates to become the next Seneschal. It makes sense why Arisens grow to have more god-like abilities closer to the endgame. They're practically geared up to be the next God.
This also makes sense why Pawns only follow Arisens. An Arisen and their Pawn is essentially the same as the Seneschal and the world's people. An Arisen's Main Pawn is basically like the Arisen's Beta version of a God creating a human. They lack the abilities of a true Seneschal to create true life and as such, Pawns are not fully humans and lack a will & personality. To compensate for their inability to create life, Arisens then would gift their pawn a piece of their soul because that's all they have. It also gives a new meaning to the act of Bestowal of Spirit (which only fully happens with an Arisen dies and the pawn is left behind); that the Arisen has successfully created true human life.