... Well, this is apparently not a popular opinion, but my favorite is Registeel. Mainly because I remember battling it with my friend and both of us marveled at its defense, able to take pretty much anything we could dish out.
But, my own life's history aside, I like it because it's a Steel-type legend. Up to that point, one did not exist and that's pretty cool. Now there's Registeel, Dialga, Heatran, Arceus (if you count that), and Coballion. But back in the days when I got Sapphire, these Pokemon didn't exist and that Pokemon was the only legend that was Steel so far. I guess I could say that about Regirock as well, but I just don't like its design as much. XD