I have been playing pokemon since Yellow,
although I actually haven't played Black/White 1&2.
My favorite games where Gold/Silver and Sapphire/Ruby,
Gold just had a lot of my favorite pokemon and a great region, (and the first region to boot!)
and Sapphire felt so revolutionary in how everything functioned in a much better way,
it also had a great region, good pokemon, lot of extra content, and graphics I just love!
(The remake of Gold is amazing, (Which is known as "Heart Gold")
and the next game in line for a remake is sapphire, so I am looking forward to it of course.
X/Y are also pretty amazing considering how it's basically fully 3D.
My favorite starter would be totodile from Gold.
I am not really sure what my all time favorite pokemon is though.