It's Team Rocket for me. I found with team galactic that their goals and objectives were just to farfetch'd. I found that the goals of Team Rocket; stealing and abusing Pokemon to turn in a profit and eventually conquer the world were much more evil than that of Team Galactic's: opening another dimension with the help of two orbs and a few stolen Pokemon. Although, it was easy to follow the plans of Team Galactic's for the most part, I found in some situations that I had no clue where I was, where I was going and why I was there.
I also liked the fact that Team Rocket has the strength and power to rebuild and regroup in Johto after their defeat to Red a few years prior in Kanto. I do admit though, that the presence of Giovanni is missed, since I always found him so fun and challenging to battle - mainly because he was the toughest and the scariest of all members of Team Rocket. Interim Boss Archer was still a good boss, but not as good compared to Giovanni because I found his Pokemon waaaay to easy to defeat.
And with Team Rocket, I loved how Gamefreak kept the nostalgic areas of the journey to defeating the criminal organisation fresh yet true to the original(s). For instance, where the player has to travel within the Goldenrod Underground and enter the locked door in the dark alley. The puzzle within was kept original besides the obvious graphic update. I could always remember as a kid, I'd get stuck on the puzzle in that room, I'd battle the theives and yet still I couldn't work it out. When I eventually did, I lost to a Team Rocket Grunt and her Vileplume. Those memories I really enjoyed somewhat experiencing again while playing through that part of the game in HGSS. And like I mentioned beforehand, the added features - though really small - really made an impact and really spurred my ongoing interest in the game and in that point of the game. The scene where we had to dress up as a rocket to infiltrate their radio tower HQ was really fun to do, although simple and when I was caught as a result of Silver, I couldn't help but scream with anger, haha.
td;lr: Team Rocket.