Goku and Vegeta rank among the strongest characters in Dragon Ball Z. It seemed only natural that they would one day combine their powers into a fusion. However, the continuity of DBZ's future, ever fraying, produced two ultimate forms of this fused state. Dragon Ball GT culminated in Goku and Vegeta, as Super Saiyan 4s, fusing into Super Saiyan 4 Gogeta. On the other hand, Dragon Ball Super saw two Super Saiyan Gods -- also known as Super Saiyan Blues -- fusing into Super Saiyan Blue Gogeta.
Both rank among the strongest characters in Dragon Ball history. However, if the two were to somehow confront one another, which one would emerge on top? It's hard to compare the might of Super Saiyan 4 Gogeta to that of Super Saiyan Blue Gogeta -- but it is possible to determine which one would win, albeit in certain circumstances.
Which is Stronger? Super Saiyan Blue or Super Saiyan 4?
The first component to determine is whether or not Super Saiyan Blue is stronger than Super Saiyan 4. When Goku fought both Beerus and Baby Vegeta, he first took the form of a Super Saiyan 3, his strongest form up until that point. Both times, Beerus and Baby defeated him in this form. However, in his kid form, Goku couldn't sustain SSJ3 for a far shorter period of time. But even then he posed more of a threat to Baby than adult SSJ3 Goku did to Beerus.
Upon transforming, Super Saiyan 4 Goku managed to beat Baby Vegeta -- albeit with help from his friends and Majuub. However, Super Saiyan God Goku managed to push Beerus, who is undeniably stronger than Baby Vegeta. Even so, it's clear that Super Saiyan God and Super Saiyan 4 are comparable in terms of power. Super Saiyan Blue, however, is a stage beyond.
It stands to reason, then, that Super Saiyan Blue as a form is significantly stronger than Super Saiyan 4. It would be like comparing Goku's base form to his first Super Saiyan form in terms of power. That's a conservative estimate, of course, because at no point did Goku's actions break the boundaries of reality like when he first turned Super Saiyan God, let alone Super Saiyan Blue Gogeta's fight against Broly.
Are Goku and Vegeta Stronger in Super than in GT?
Every recipe is as good as its ingredients, so the two Gogetas will be only as powerful as their two fused partners. Are Goku and Vegeta stronger when they fuse in Dragon Ball Super, or when they fuse in Dragonball GT against Omega Shenron? Again, the answer seems obvious: they're stronger in Super.
By the time they fuse into Gogeta in Super against Broly, they have already participated in the Tournament of Power. Goku has achieved his Ultra Instinct form, which can only be gained through intense training and mastery of skill. He and Vegeta have trained under Whis, who even trained the literal God of Destruction Beerus.
By comparison, Goku and Vegeta in Dragon Ball GT haven't come close to that sort of power. However, GT is notoriously inconsistent with its power levels. Super Saiyan 4 Goku gets blown away by Omega Shenron, while base Kid Goku supporting a Spirit Bomb can take rapid-fire blasts of the same intensity without flinching. However, both Goku and Vegeta are definitely less powerful here. They have yet to match the power of a God or reach Ultra Instinct, and both seem genuinely less fit as fighters.
Let's Factor in Super Dragon Ball Heroes
The untouched element to this debate is the non-canon Super Dragon Ball Heroes games and animation. Xeno Goku is an alternate universe version of Goku, similar to Dragon Ball GT Goku. In the anime's opening, we watch as Xeno Goku confronts Goku, fresh off the Tournament of Power. In this fight, we see how Super Saiyan 4 Xeno Goku is on par with Super Saiyan Blue Goku. Blow for blow, they cancel each other out.
Granted, in Dragon Ball Heroes Goku is capable of using Ultra Instinct, which might push Super Goku over the edge. However, Xeno Goku unlocks an extra form of Super Saiyan 4 when fighting Black Janemba: the Super Full Power Saiyan 4 Limit Breaker. This, again, puts the two Gokus on par with one another.
Dragonball GT's Super Saiyan 4 Gogeta stands no chance against Super Saiyan Blue Gogeta. But Xeno Gogeta, given the incredible power of both Xeno Goku and Xeno Vegeta, would certainly match Super Saiyan Blue Gogeta. The winner, ergo, could go either way, depending on which of these evenly matched fighters pulls out the better strategy.