I don't know if he's the absolute most powerful. But he's got to be one of the top pound-for-pound. Physically, he's smaller than Hesei Godzilla, but in my opinion a much scarier and ruthless combatant. Hesei Godzilla was slower, didn't really look too impressive until he A) body slammed Ghidorah and B) ripped open Destroyah by using claws and his head. GMK Godzilla was a very capable fighter, always going for the kill-strike, was quicker, more cunning and remarkably aware (when he batted Mothra out of the air like a fly swatter without even facing her while chewing on Ghidorah's neck, ducked Baragon's leap last second and hit him with his tail like Robinson Cano, or swung Ghidorah's body into the torpedo attacks).
I think GMK's ray attack is also stronger than Hesei Godzilla. He made a giant mushroom cloud and obliterated his opponents when he usually caught them point blank. That says something about it's force. Hesei Godzilla would spam it, most of his fights were like games of Atari of just ray attacks back-and-forth, an typically Godzilla would fall down before any of his opponents. He rarely hurt his opponents with just his ray until he A) absorbed enough energy to "power up" (orange spiral ray) or B) did it like a hundred times (after getting help) and the opponent finally gave way and succumbed to it.
Durability I'd also give to GMK. For one, he's the embodiment of dark spirits, so in essence I just think he keeps coming. Sure, you can argue that Hesei Godzilla faced tougher challenges, but he also lost a few of them. Some say Biollante beat him (although I don't buy this, to me it looked like Godzilla was drugged up but he still kind of finished her), beat by Mothra and her pixie dust (I hate Mothra), killed by MechaGodzilla (needing Rodan's help), almost beat by Space Godzilla (needed Moguera's help), and barely beat Destroyah even as Burning Godzilla. Now, none of the monsters in GMK had massive offensive power, but Godzilla beat them all handily and on his own so I can't knock him for that. And Mothra in GMK was way quicker than Mothra '92 and Godzilla whooped her and Ghidrah (plus the military) like it was child's play. It's like what you say as a boxer--they only fight who is put in front of them and you can't argue with someone who beats them all and goes undefeated.
Now, his disadvantage (aside from being shorter than the other incarnations, except the other millenium Godzillas) is the regeneration factor as others have said. Since he's a vehicle for angry souls, he may not even regenerate in the same fashion. We are led to believe that GMK Goji took 50 years to return after 1954. And while I wholly believe that the entire point of showing his heart beating on the ocean floor (with the epic Godzilla music beginning to play) was to tell you that GMK Godzilla cannot be killed and will return, in time, I think it takes a while. May even take another 50 years. So, it's in his best interest to stop getting blown up.
Burning Godzilla probably withholds the most raw physical offensive power, but that's because he's literally seeping overloaded radiation from his pores. If you take all the Zillas, make them the same size and have them all fight to the death, I think GMK Godzilla is the last one standing. He's too good of a claw-to-claw fighter and he's cunning--in a Dark Knight Rises Bane kind of sinister way. He'd bite necks and tear jugulars apart. Sure, they will all regenerate and return, but GMK Godzilla still "won" in my opinion. Atleast he wins in the "skill" department (although Showa Godzilla learned to fly, shuffle his feet like Muhammad Ali, and do some judo techniques
so that might be interesting).