I would say it's a tie between the first three starters for me. I love all three so much that I can't pick my favorite among them!
I'm in the same boat for the Original 3 as well. I love all three of them and they're so near and dear to me that I can't choose.
Although for the other games I do have my preferences. xD
H.Gold/S.Silver: Chikorita
Ruby/Sapphire/Emerald: Mudkip
Diamond/Pearl/Platinum: Piplup
Black/White: Oshawott
X/Y: I am in the same boat for the originals. Although that may change when we see their evolutions. haha