If I remember correctly, the Magikarp line is based on a Japanese folktale about a fish dreaming of swimming a waterfall, from bottom to top. Through trial and effort, the fish reaches the top, but emerges as a sea dragon (or something) in triumph of his achievement. So there's basis to Magikarp's drastic evolution.
I don't know if it's the same for the other two lines you mention. Probably have to Google that.
They knew their priorities, that ol' Game Freak. Putting the focus of the story on an evil race of pompous Gaga drag queens incompotent of pulling of plans that support the real goal of Lysandre.
Galactic are no different either, to be honest.
Yeah, there is a thematic there for Magikarp (and Remoraid, though many tend to forget it), it's more that I was trying to point out that it's not the first time a Pokémon has jumped in design to fit a thematic. Magikarp jumped because of that folklore, Remoraid jumped because they were trying to go for a revolver to cannon theme, and there are a good number of other examples like that as well. Samurott, while maybe flawed in that execution depending on your viewpoint, isn't the first to jump using a thematic like that, the designer probably wanted a bulky shogun and felt that changing animals was a good idea for that motif over sticking with otters. I can see why it may've not been appealing to do that, but I don't think it was lack of creativity that it happened.
As for Dragonair to Dragonite, they don't really have an excuse unless you count sea serpents as dragons. Personally, it always surprised me that Dragonair jumped from a sea serpent motif that it and Dratini had to traditional anthropomorphic dragon like Dragonite.
As for Team Flare, yeah they were pretty lackluster. Galactic was a bit better IMO though, mostly because as @
Rysir
said, Cyrus was trying to manipulate them in the first place, which would explain that disconnect. Lysandre was intending to repopulate the world with his team and they were fully in on it, which doesn't really make sense considering how much more self-absorbed they are then him and don't really go along with trying to make the world a better place.