A lot of fights between one character and another come down to one character having a serious advantage in one way or another, but this fight is one that would be won in a very different manner, especially if the version of Thanos being used was the one from the comics rather than the MCU. The MCU version is tough, there’s no doubt about it, but he wasn’t the death-worshipping madman that the comics introduced to so many people, and it’s fair to say that Goku would stomp that version since as resilient as the MCU Thanos is, he’s not the cosmic-level threat that his comic book counterpart is. If Goku were to take on the Gauntlet-wielding comic version there’s no doubt that the battle would be long, pitched, and anything but easy for either combatant, but in the end, Thanos would win. Some folks don’t even like the attempt to pit an anime character against a comic book character since like it or not, they are very different, but then again, they’re both fictional characters, so it shouldn’t matter where they come from.
In neutral territory, where both could call upon every single one of their powers, and yes, giving Thanos the Infinity Gauntlet, Goku would find that he didn’t have the stamina or the intelligence out outlast or outwit Thanos, since the mad titan is the kind of character that doesn’t enter a fight without thinking about the variables that might affect the outcome. Given enough prep time, it’s fair to say that Goku would…train really hard and still lose. But Thanos would study his opponent and discover ways to circumvent the most obvious threats that Goku could launch at him and find a way to either neutralize or weather and counter the attacks that Goku is capable of, since one thing Thanos is good at, among others, is finding a way to outfox his opponents.
There are plenty of Dragon Ball fans out there that are bound to shake their head and say ‘no way’ when it comes to this battle, especially since Goku, at his best, is a character capable of destroying planets and galaxies alike. The problem is that Thanos is about the same in the comics, and he’s capable of such massively destructive feats that he’s been able to imprison a galaxy and several cosmic beings at once while assuming the role of Eternity at one point. Goku is capable of many incredible things, but the fact is that when compared to Thanos, he’s not capable of outwitting the mad titan. This is one of the elements that would sway this fight, as durability isn’t an issue with either of them since they’ve both taken on extremely powerful opponents. Stamina would be another issue for Goku however, since switching from one form to another takes a great deal of stamina, and in a fight with someone like Thanos, stamina is not something a person wants to be short on, since the mad titan can last for a while, and since he doesn’t have to keep powering up, as he’s capable of stretching a fight out as long as he needs to, as he usually has one failsafe or another that he can fall back on and many contingencies that can help him in just about any fight.
There’s nothing to take away from Goku since he’s tough and relatively intelligent, but he’s not as cunning or as devious as Thanos in any way, shape, or form. The fact is that even without the Infinity Gauntlet, Thanos has taken on a few heavy hitters in his time and held his own if not stood victorious when it was all said and done. Without the gauntlet, the fight might be much closer than many would realize, but it still stands to reason that if both had prep time that Thanos would be victorious since what Dragon Ball fans might not want to hear, especially if they’re of the mind that anime and comics are not equal, is that Goku is not as intelligent as Thanos, and thereby he’s bound to pummel the mad titan as much as he can, without realizing that Thanos is willing to take a bit of punishment to lure someone in.
When all is said and done there’s no such thing as an honorable fight with Thanos, since he’s bound to take the advantages as he sees them, and it’s easy to state that he’s going to press every possible advantage as much as he can. Honor and dignity don’t factor into a fight with Thanos that often, especially in the comics since he’s a death-worshipping madman that’s often bent on one design for domination or another. Goku is capable of calling upon the type of power that could seriously tax and even destroy the MCU version of Thanos, but pitting him against the comic book version would be a mistake since all the power that he can summon wouldn’t be enough.