I think you want to look at the cycle DPS, which includes quick moves combined with charge moves. Some quick moves will be better with different charge moves. In your specific example, I think it is just a case of bullet seed being that bad of a move. Razor leaf has almost double the DPS when you factor in the double SE stat against Rhydon.
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Prestiger Quick moves: EPS vs. DPS
Since Gen2 I mostly prefer high EPS quick moves to charge as fast as possible the buffed charged moves.
But yesterday I realised something while I was prestiging against a Rhydon. First I used a 1100 CP Sunflora with RL/SoB, super strong prestiger btw. It took 1/3 of the Rhydons health, then fired SoB und finished the job with one more hit before it got it's Megahorn off.
Then I tried the same with a BulletSeed/SoB Exegg. It charged SoB much fast than Razor Leaf but that was'nt exactly an advantage in this fight. As soon as I fired SoB, the Rhydon still had about 1/4 of it's health left and countered me with Megahorn before I got to finish the job.
So my question: Is DPS for prestigers quick moves more important than EPS?
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Answers
As others have said, it depends on the moveset and the full rotation damage.
Also in play is battle tactics.
If you held off using your SoB with your BulletSeed egg, then you could have done more damage, without doing enough to give the defender energy to use their charge move. That is, simply use your quick move for longer and deal more damage before unleashing SoB.
Once you unleashed SoB the defender would have gained a lot of energy from the damage done, and so would have been able to fire their charge move faster than if you had held off.
Holding off on the charge move for a little longer would enable you to finish them with a charge move, without the defender gaining enough energy to use a charge move.
You need to adjust your style to suit the moveset you are using.
