The first time through, I chose Treeko simply because I loved it in the anime. But the most recent time through, I chose Mudkip, as it is clearly the best. Being a Water-Ground type Pokemon means it has STAB with both Surf and Earthquake, making it extremely potent. It can also learn Ice Beam as soon as you find the TM, which along with maybe Hydro Pump or even Dynamic Punch make a great Pokemon. Additonally, it made the game easier, as due it's duel type, Electric Type moves did not effect it.