Battle-wise: Gyarados has a double weakness, and I prefer staying far away from anything with double weaknesses when picking Pokemon for the Battle Frontier. Milotic is a wonderful Pokemon to battle with - good defenses AND special attack, and it can learn Recover.
Design and personality-wise: Gyarados reminds me of Charizard in a way - they both try to look cool, but end up looking horrible. It's one of those annoying GROARGH FEAR ME Pokemon who I dislike immensely. Milotic on the other hand, while being a bit too stereotypically pretty for my tastes, apparently has a calm and friendly personality, which is awesome.
So yes, I obviously prefer Milotic.