Thanks guys!
That's a hard one! I feel like Flygon might be my favorite but there are many others that are very close. As to why, it would be because of how much I used it when I was younger, it's beautiful design and the nice memory I have of it in the Jirachi Movie, even though I do not remember much of it.
Here are too many honorable mentions:
Lapras, Flareon, Bayleef, Quilava, Croconaw, Quagsire, Tropius, Breloom, Ralts, Slowbro, Sandshrew, Jirachi & Entei.
They are all here for a different reason.