Tl;dr: It's all up to you, but don't judge the strength of the skill by it's Attack power alone. Water Pulse is weak but quick to charge, the best skill (Hydro Pump) requires you to be a better player to use.
On viewing Vaporeon's skills, Water Pulse is weaker on use, but have more uses out of it compared to it's other abilities:
The following information is from here: http://www.pokemongodb.net/2016/05/vaporeon.html
Vaporeon Fast Moves: Vaporeon Charge Moves:
Water Gun Aqua Tail Hydro Pump Water Pulse
Power: 6 Power: 45 90 35
Cooldown: 0.5 sec Cooldown: 2.35 sec 3.8 sec 3.3 sec
Energy: 7 Energy: -50 -100 -25
DPS: 12.0 DPS: 19.1 23.7 10.6
What's clear here is that while it's two other moves are higher in power, their charge requirements means that you'll need to survive longer before they can be used. The DPS on the bottom shows that it's more efficient to use the stronger attacks, but that's still under the assumption you're able to get that charge going constantly. The real DPS per attack is going to be much lower in real world settings as you (as a player) will miss attack opportunities/get hit often.
In theory, you'll want to get another Eevee and hope that your next Vaporeon get Hydro Pump to get the best move-set possible. for now though, Water Pulse is good since you'll get to practice using Pokemon skills more often.