They all had their weak and strong points.
The rockets were kinda... eh. They didn't have any purpose whatsoever. They were evil because they FELT like it - because they were greedy assholes and nothing but. I appreciated Giovanni, in-game, as he was a man of honor, even for a leader of an evil group. And him being the eight gym leader was a very interesting twist that I didn't see coming back when I first played Red all these years ago. G/S/C's Team Rocket Redux were an interesting idea, but weren't so well pulled off, in my twisted opinion. Most of G/S/C was sub-par anyway, though, so all good.
Magma and Aqua only got to shine in Emerald, where their story-lines was integrated, otherwise they were just rivals-and-mirror-images-of-each-other. Their leaders believed they were doing good for the world, by any means necessary, and that their opposing numbers were dangerous eco-terrorists. Only when they upset the balance of the world they realized that they were only causing damage and they decided to disband their teams and do what they can to set things right. This was, to me, their finest hour. Ultimately they were useless because a ten-year-old brat HAS to save the world, this being a PokéMon game and all, but yeah. >>
Then you have Team Galactic, who have the stupidest outfits and are generally the best comic relief I've had in a PokéMon game in YEARS. They have no idea what their goal is themselves, they're just in this because it pays them money and because they were told that Team Galactic will create a better world for its members. The galactic Commanders, Saturn, Jupiter and Mars, just had fanatical devotion for their 'Visionary' leader, a madman who believed that humans, war and strife were bringing down the world - and therefore wanted to collapse time and/or space and re-create a new one in his image, where he shall rule and rid the world of war and strife. God complex? Oh yes. I guess he meant well in his own twisted misguided way. But... Yeah. Cyrus always strikes me as the first genuine dangerous madman that PokéMon ever had, which will forever give him a place of honor in my pantheon of game villains.
So yeah. They all have their stories and epic internal struggles - except for Team Rocket who, in-game, is the most boring organization I've ever set my eyes on. I suppose however, that the anime is making up for it, as the anime's goofy, misfit Team Rocket Trio are definitely one of the things that make this silly series watchable...