I been looking at smogon list(the king of pokemon society)
and all the OU and ubers are mostly ugly. only latias, latios, vaperon, and dragonite are cute.
I dont know why Milotic is in UU she is loads better then vaperon(unless, it's a timid nature)
I'll give you three reasons why to use Vaporeon.
1) Wish.
This little thingy restores 50% hp on the next turn, even if it is a different poke that used it. Meaning that if you have a Vaporeon that used Wish, and switched in, say, Lucario, on the next turn Lucario would recover 50% of its HP without doing anything! That is incredibly useful due to all the "extra damage" that floods the game, such as spikes, stealth rock, leech seed, sandstorm, life orb, and so on... Wish is invaluable, to put it straight.
2) Water Absorb.
A Gyarados that has Dragon Danced does up to 34% to a Milotic with Waterfall, Vaporeon avoids all that. It has an immunity to one of the best offensive types in the game, that alone is good reason to use it.
574 Atk vs 282 Def & 394 HP (80 Base Power): (28.93% - 34.01%)
3) Grass Knot.
Milotic eats loads of damage from a 100 Base Power Grass Knot due to its weight.
Vaporeon recieves only a 60 BP Grass Knot since it's way lighter, giving it a slighty higher staying factor, whilst also making it a very good Infernape counter.
Don't forget that Vaporeon also can Baton Pass 101 HP Substitutes, and can haze/roar away status boosts.
That's probably why Vaporeon is used over Milotic.