In the anime Giovanni has undergone a gradual change from Evil genius to Comic relief and I personally find it boggling. The concept of "Boss Fantasy" has evolved from a simple view of Meowth sitting on Giovanni's lap to Giovanni parading around in a little black Speedo. In the Manga, Giovanni is portrayed as a ruthless criminal leader who would not hesitate to destroy a little ten year old boy, where in there anime he is hardly seen except for in these new fantasies.
The earliest of the fantasies is in episode 215, A Corsola Caper. Meowth wishes to get Giovanni a slew of Corsola for him to decorate his house. These fantasies start out innocent enough but as the years pass by they just get more and more bizarre. In the early fantasies, Giovanni has somewhat normal roles or reactions, like petting Meowth instead of Persian. This is not as wild as riding on the back of Deoxys in outer space or running through the wilderness covered in honey.
I have a few theories for why this has happened over the course of the years. My first theory is to take anything "scary" out of Pokemon. Since Pokemon is aimed to be a children's show, TV censors would not like to have anything scary or to have anything harmful or compromising happen to the main characters. (For example, the Dratini episode was banned due to the fact that a man held a gun to Ash's forehead.) Therefore, having an evil archenemy is completely out of the question. Having Giovanni point a Beedril's arm or even a weapon at the main character would be completely edited out. So to keep Team Rocket's boss in the storyline and to keep him from being a scary archenemy figure, they deluded him down to a comic relief. It has become an ongoing gag where Meowth has a fantasy about what they can do to please the Boss. This gives and image of Giovanni that is not scary or intimidating to young viewers.
My other theory is that, since the show is loosely based off of the games, Giovanni has no real role anymore. After the first generation games, he has completely left the scene. However, in the anime, Jessie, James, and Meowth still work for this mysterious Boss person. So, in order to keep him in the anime, they put him in during Meowth's fantasies. I personally miss how he used to be a villain in Shadow, he added that sense of good versus evil to the anime. Now, instead of having that overlying theme, the anime has become focused simply around the main character's goals and achievements. I can say that I enjoy both versions of Giovanni and it is fun to watch the older episodes to see the drastic change in the presentation of his character.