Honestly, Team Rocket is the only one I've ever taken seriously. :/ Since the team is based on crime syndicates/gangsters, it makes sense and it's believable.
And then you have Aqua and Magma, who just had stupid goals. They were trying to... raise the ocean's levels or get rid of it. Ooookay. Who would even follow ideals like that? It makes no sense. And Galactic was a cult, so it's a little more believable but their goals still don't make sense. I never felt threatened by them, it just felt silly.
As for the Ranger enemies... they were always just so bumbling that you couldn't take them seriously.
So by process of elimination, really, TR is my favourite. (But I still like them regardless.)