I’ve been playing for a few days now and I’ve found that (unless there is a cap on the trainer level, which I still don’t know), the most powerful Pokemon is whatever it’s easy to catch the most of for you personally.
This is because you can transfer all but one to the professor to get the most candy for that Pokemon type, which means that you can level up that Pokemon type more than any other, making it the most powerful.
Initially I suspected that more powerful Pokemon would be the rarest, but this doesn’t seem to be the case. In the future, it may develop that there’s a trainer level cap, in which case there may be some Pokemon that get more CP or HP per level up and become the most powerful when they reach the level cap. At the moment however, it seems that the most powerful Pokemon is whatever the most common Pokemon is.
In my case, the most powerful Pokemon is a Golbat.
Secondly, it’s worth noting that Pokemon Go does operate like a game of Rock, Paper, Scissors. Some Pokemon types are more powerful against others.