Strength. I won't argue that Superman has immensely higher physical lifting strength than Goku does, that's completely accurate. Superman emits a telekinetic field around whatever object he lifts, allowing it to stay in one pieceāhe was pretty much designed specifically for heavy lifting.
Where the discrepancy comes is the assumption that physical lifting strength IS punching strength. That's not at all accurate; martial arts require explosive strength, not gross lifting ability. The Z fighters use their Ki to enhance the force of each blow, both in speed and power, filling their punches with huge quantities of energy as they swing them.
I'm not talking about energy attacks, I'm talking about normal punches and kicks. It's all about how the energy is released. Goku's punches are far, far, far more powerful than Superman's.
For current Superman, I'd estimate that Super Saiyan Goku's punching strength is more than enough to outmatch him. For the others (Pre-Crisis, Silver Age, Superboy Prime, etc.) it would take a quite a bit more than just basic Super Saiyan. Speed.
There is a huge difference between top speed and battle speed. Superman's flight ability is FAR superior to Goku's, as we all know. He expends no energy whatsoever, and can fly at much faster speeds for long distances.
But what he can't do is simply start off at that speed, or anywhere near his top speed for that matter. He has to build up to it. That's where Goku has a huge advantage.
His battle speed, the agility he has at any given moment to dodge, is leagues above Superman's. By clearing his mind, Goku can teleport over short distances quickly enough to evade anyone who isn't as fast as him...and that's not even talking about Instant Transmission. In DBZ this is huge, as shown when Ultra Trunks tried to beat Perfect Cell.
Cell was untouchable simply because of his superior speed and agility. So, in a battle up close, Goku would have a clear speed advantage. Fighting Skill.
Just watching his animated fights or reading them in the comics, you see a clumsy brawler who is entirely focused on power punches. Seriously, if he had any kind of real fighting skill opponents like Doomsday or Darksied would be absolute pansies that couldn't touch him. Plus, if he could move at his top speed during battle he could just dodge all their blows, since his speed FAR surpasses theirs.
But no! He doesn't...he gets owned like a little ***** every time! Imagine if Goku fought those guys.
He would get bored in the first minute. His fighting skill should be considered unequivocally superior, and that goes for about anyone in the DC universe, even precogs. The problem with Superman comes when you actually have to kill him, though.
Writers won't let him die for real, which is a huge cop-out. His actual regeneration isn't any superior to Buu or Cell, he just has this extreme natural defensive construction. It seems like no amount of beating is too much for him, and that his body will always repair itself.
I see this as the only real obstacle for Goku to overcome. He would need to finish Superman in the same way as Cell or Buu, by destroying every single atom. The trick to that is just a big enough Kamehameha.
Good news is, with Goku's favorite move, the Instant Kamehameha, this is more than possible. He would just need to power up and make his one shot count. Otherwise, the fight would drag on and he would lose energy while Supes would just keep healing from the sun.
But that is at regular Super Saiyan. I don't imagine Goku needing more than that, as I personally believe Cell could pwn Superman into the next dimension as well, and don't get me started on Buu (even without absorption).
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