Alright, I won't necessarily say my favorite... because I don't really know.
But the one thing I loved about the original red version was that it felt more rugged. In that shade of red, everything looked hardcore. The whole thing with seeing the ghost of the marawak was pretty cool and dealt with death of pokemon much stronger than the others. (except black and white I have not played yet. College life is busy when your stupid and don't plan time out well enough.)
And I mean look at mewtwo. How does he compare to all other pokemon? He is a science experiment gone wrong. Look at him, he's got a tube connecting his head to his back. He is completely insane. And yes, it may have been many years ago, but I loved the first movie.
On top of that, I liked the gym leaders more. Maybe it was because of the show, but the original gym leaders and elite four were far more memorable to me.
What can I say? After everything has been getting cuter and cuter, some of the original guys, especially in their own pixilated pictuers were simply rougher and tougher. ... Or at least I think so.