CP

Because the 3 different stats have different weighting on your CP, or in other words, 15 attack IV (usually) gives a different amount of CP than 15 defence or stamina.

CP gain due to IVs is dependent on the relative increase to the base stat, and if the stat is stamina or defence, the relative increase is then square rooted to get the CP increase, because that's how the CP formula works.

This means that increasing a stat that was higher to begin with generally less effect on your CP than increasing a lower stat.

For example, 1 attack IV on a Chansey will increase it's CP more than 15 stamina IV because it's stamina is already high and also because it's attack is so low.

In your case I'm guessing the higher IV Vaporeon has higher stamina and less attack than the lower IV Vaporeon.

https://pokemongo.gamepress.gg/pokemon-stats-advanced

CP is the attack stat multiplied by the square roots of the deffense and stamina stats (a pseudo-average of Def and Stm) multiplied by a constant for the pokemon's level.

Because of the way CP is calculated, a difference in attack has a greater impact than an equal difference in either defense or stamina by itself.

A pokemon with greater total IV percentage but not max Atk IV can still have a lower CP than the same species pokemon with higher Atk IV.

https://pokemongo.gamepress.gg/cpcalc#/
An extreme example, using the CP calculator, two hypothetical Vapoeeons at level 30:

15 atk / 0 def / 0 stm
2526 cp, 190 hp

0 atk / 15 def / 15 stm
2521 cp, 201 hp

I understand the CP formula mechanics, but this is another dimension which is necessarily complex. Better IV = Better max CP would make much more sense.

I also hate that I have mons with roughly the same IV and a lower level mon has higher CP than and lower level mon.

If "CP" is meant to be the measure of battle quality (damage and duration), then what does IV actually mean in this case? It is a better pokemon for what purpose, sitting in the pokebox?