I liked how they returned in GSC and were trying to get Giovanni to come back, they were intergrated well into the region of Johto, with the Slowpoke Well, Radio Tower, Mahogany Town etc! That being said, they were laughably weak at the Radio Tower, but that was a problem with the Johto level curve which was at fault for a couple of the games' issues. Also, I liked the Celebi event with Team Rocket & Giovanni in HGSS, that was a nice extra :)