Please read this: https://pokemongo.gamepress.gg/damage-mechanics There are at least one of these questions every single day with the same answer.
I don't know if you are talking about defensive or offensive moveset here, but Flamethrower outperforms Heat Wave in both of them. They are rather close to each other when attacking, but for defense Flamethrower is clearly better.
To make it simple:
Quick moves are rather weak compared to charge moves, therefore you want to be spending as much time casting charge moves as possible (this is especially true for defense because of the added 2 seconds between each fast move, but often not the case when attacking because of the plain difference in DPS. It all depends on the Pokémon and the moves). Even though Heat Wave's DPS is slightly higher per single use, when you use Flamethrower you will be using less Ember thus making your overall DPS slightly higher.
For example, let's say you have filled your energy bar using Ember. When you use Heat Wave once, you are back to using Ember, however, if you have Heat Wave, you get to use 2x charge moves instead of using the weak Ember making it slightly more efficient.
Please note though, that for offense Fire Blast (even despite being a single use charge move) is still the best charge move because the DPS of the move is just so much higher.
