Actually considering interdimensional travel was the plot of not one but TWO later antagonists (Team Galactic in Sinnoh and Lusamine in Kalos), it fits in really well with Pokemon. (I can't believe Nintendo ripped off a twelve-year-old's fanfiction for TWO later plots.)

eta: Team Rocket are actually the least ridiculous organization in Pokemon canon. They're basically the Pokemon mafia. That's it. It's the Hoenn and later teams when they started to get a bit weird.