Bradford having F.O.W.L. agents work in pairs when it comes to Missing Mystery missions makes sense considering how many of their agents are Wild Cards and have their own agendas so forcing them to work together not only gives them a better chance against Scrooge, but prevents them from working their own angles against F.O.W.L.'s better interests.
Of course, Pepper is a very interesting choice to partner the Phantom Blot with; the others don’t seem to get their operations require complete deception and 100% Plausible Deniability. Pepper may be an Egghead, but out of all of them, she actually follows the rules and cares to pay attention to the organization’s goals, and is able to think on her feet. That being said, Pepper shows a lot of promise as a potential agent as she has the qualities Director Buzzard is looking for, and it would be in his best interest to set her up to be the Phantom Blot’s apprentice.
Some have complained about Webby being too forceful in trying to make this visit to the castle as best as it could be. However, consider "The Secrets Of Castle McDuck", where she was in such awe and splendor that she spent most of the adventure stiff as a board and missed out on the adventure. She just wants to make sure she won't miss out on anything.
Aside from his hatred of magic, the Phantom Blot was a pretty good choice as a villain for this episode. It focuses on the importance of family, and how a family may fight, but they'll always have each other's backs in the end. Phantom Blot's entire family was killed when Magica destroyed his home, and as a result, he's closed-off, harsh, and cruel. Pepper tells him she's the only Egghead who was willing to work with him, and he's visibly hurt. Obviously, Blot needed to relearn the lesson about family as much as the McDucks did.
Louie being one “great” over when referring to his great grandmother Downy might seem like an error on the writers’ part, but knowing Louie, he’d be easily confused by the family structure that he’d stop keeping track of generations after Scrooge. As Donald said, their family relationships can get really confusing.
The age gap between them also makes it easier to make the mistake (the family skipped two or three generations due to the immortality stones).
Webby not realizing that she shouldn't be butting into the McDucks's fighting makes sense when you realize that since she's an only child, she wouldn't realize that Sibling Rivalries are perfectly normal and common.
Fridge Horror:
The Phantom Blot going after the Blessed Bagpipes has some dark undertones when you remember F.O.W.L.'s goal of ending Clan McDuck. If the plan involves actually killing the family members along with their friends and allies, then F.O.W.L. is taking precautions by stealing an artifact that the heroes could potentially use to bring the fallen back to life. Taking the bagpipes away from Clan McDuck would ensure that any deceased family members would be Killed Off for Real.
