My favourite gen is the third most assuredly. R/S/E were incredible, music, Pokemon, area design, atmosphere.. They had everything. 3rd also had FR/LG, Colo/XD and started the best spin-offs in the series (PMD); it's a no-brainer that 3rd wins for me.
In saying that however, I would recognise that B2/W2 are the highest quality games in the series, they had so much content, so many Pokemon to catch and a good story. Even if I do love Gen III waaaaaaaay more.