Gen 1: Gyarados
It's always been one of my favorites from Gen 1 all the way up to now, and one of my fondest Pokemon memories was dominating the battle tower in Diamond with a Dragon Dancing Gyarados, plus it evolves from Magikarp, which for me, carried a message that there's great potential in even the weakest of us. As for my favorite back during gen 1, hands down, it was Aerodactyl, which is still one of my favorites today.

Gen 2: Scizor
A cool pokemon that evolves from the equally cool Scyther? And gets access to a Technician-booseted Bullet Punch? Yes please! Kingdra was my favorite back then, mostly because I was disappointed when I found out that Gyarados wasn't Water/Dragon.

Gen 3: Flygon
Was Flygon, still is Flygon. Always liked the design, and was pretty upset when it was made irrelevant by Garchomp.

Gen 4: Gallade
Gardevoir was one of my favorites from Gen 3, and her male counterpart quickly became one of my new favorites. Also, calling Gallade my Gen 4 favorite is saying quite a bit. As far as Pokemon go, Gen 4 is probably my favorite, with Pokemon like Lucario, Electivire, Leafeon, Glaceon, and so many others. And yet somehow, it wasn't that hard to pick a favorite

Gen 5: Zoroark
The first Pokemon introduced in Gen 5 is also my favorite from that Gen, due to its unique ability. I didn't actually use one until Gen 6, so I had a different favorite during Gen 5: Galvantula. A spider that can electrocute you sounds like the stuff of nightmares.

Gen 6: Noivern
Because, well, it looks cool. It was a good enough reason to like Gyarados and Aerodactyl back in the day, and is still as good a reason as any.

And the winner is....

I'll have to go with my favorite pokemon from my favorite generation: Gallade.