I'm trying to get a Lapras for one of my Warriors as their Perfect Link, but I've yet to find one. I'm on Hideyoshi's story, with every single Kingdom conquered (save for Aurora, because I purposely cornered Oichi), with completely maxed-out facilities in every Kingdom.
I experienced a similar problem with Pawniard and Misdreavus in Kotaro's campaign. Despite my own former experiences and what Serebii said, Pawniard never showed up in the many kingdoms he was supposed to be in and Misdreavus refused to show up in the Lv3 Cave and/or Float Stone in Spectra. I even reloaded, like, 10 times to get them to show up and they never did. One day, though, they started appearing and they were extremely common ever since.
I suspect that some Pokemon have a hidden time requirement - you have to be so many months into the episode in order to locate them. With the exception of the intentionally gipped episodes (e.g. Kotaro's "only Dark/Poison/Ghost/Dragon Pokemon"), I am fairly confident that the random Pokemon do not differ between episodes.
PSN for Dragon's Dogma: MrDifficult (Pawn: Merritt) General Use PSN: DarkestSamus