Pokemon moveset effectiveness

You can find the best moveset for a pokemon on this site - e.g. for Vaporeon it's Water Gun and Aqua Tail.

The site takes into account not only how long the attack takes, but also the critical chance and whether the attack gets a bonus for being of the same type as the pokemon (STAB).

The difference between one bar and two bars is rather huge because you can use your special move twice as often while the difference in damage in this case isn't that significant. Apparently the best moveset for Vaporeon is Water Gun and Aqua Tail so it is ultimately up to you.

Source

Thinking between bars and damage done between moves is easier with the tool in this site: http://poke.isitin.org/ Where you can also see how good your pokemons IVs are. It displays the possible attacks that the selected pokemon can have. What you should be thinking when assessing what moves are better is the power/second for fast and special moves compared to the optimal case where they are both the best that pokemon can have. Also having different e.g. Water as special and Ground as normal attack can be useful if you happen to encounter some pokemon that is resistant to Water attacks. By checking the site in the link above you can see that Vaporeon has only Water attacks...

That being said the ideal Vaporeon has Hydro pump and Water Gun (fast).

For almost all the moves, you pick the basic move that can be used the fastest and then you pick the strongest charge attack.

You pick the fastest basic move because you want to charge your special. The timing difference between a lot of the moves is quite significant, but the DPS is almost the same, so you really want the fastest one.

You want the strongest special because your charge time is equal to 4-5 fast basic moves. Moves with 3 charge or more are usually so weak that you might as well just attack normally, unless you're triggering STAB and Super Effective bonuses.