The debate is arguable at best, but there is no definable answer. (Obviously, I'm biased toward a specific on, but that's neither here nor there)
When it comes down to it, the best thing you can try to do is break down who is able to do what, and under what conditions.
Persona 1 and 2 are set in a completely different world, where things operate on a fundamentally different system. P2EP was the last game of it's trio before the world was broken down and reworked entirely, so assuming that "They can use their persona in the real world" is not exactly viable for them, as everyone was able to manipulate the world, even if not a persona user. (Remember the rumor system?)
So, for the time being, I'm going to exclude Persona 1 and 2 MC's out of this, since their entire world was set up entirely different, and it allowed them to do much more, with a lot less.
And for the sake of arguments, I'm not using "Persona Victories of Gods" as a viable measuring stick either. If we do, Joker wins automatically as he kills what is considered the Gnostic's version of God (The God of the Old Testament).
SeeS, as far as I'm aware, are actually the "Strongest". They train outside of the midnight hour constantly, and actively have to go out and defend their targets. This one was debatable up until Arena Ultimax, where it was reveled that the SeeS were able to summon their persona out into the real world, without the need of a metaphysical realm, but it was at a massively reduced effect, with maximum effort. With that in mind, Minato is also the only user of the Universe Arcana.