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In Infinity War, Vision is useless, letting Thanos pluck an Infinity Stone from his head without resistance. Ultron slicing Thanos in half while inhabiting Vision's body shows how badly the MCU mishandled Paul Bettany's character.
However, Ultron, who was fascinated with the Stones, effortlessly killed Thanos by cutting his body in half with a laser beam from the Mind Stone and obtained all the Stones for himself which turned him into a cosmic being.
So Visions weakness was his mind. His disbelief in himself was causing the power of the stone to be hindered enough to where he was able to be stabbed, and not phase. His head was cluttered with so much negativity, that it caused him to give up his existence and be willing to die.
This alternate has an argument, and perhaps the Thanos of its universe was somehow inherently weaker than the core MCU's, but there doesn't seem to be any scenario where the Sacred Timeline's Vision could ever defeat its Thanos, who had already harnessed five of the six Infinity Stones.
Mostly, Vision is pretty much a direct copy of Superman, as he is able to fly, shoot lasers, and have super-strength. Superman could quite easily beat Vision with just these three abilities.
Since Vision was caught off-guard, he didn't have time to phase through the blade, and his synthezoid body began to malfunction. After Corvus Glaive's attack, Vision couldn't use his powers and remained badly wounded for the rest of the movie, which gave Thanos and the Black Order more freedom to confront the Avengers.
He's been an Avenger for a very long time and has faced down the Hulk before, so he knows what to expect. While there are some who would argue that Vision couldn't the Hulk on his own, the Vision definitely has the power to take Hulk down.
Additionally, Wanda demonstrated just how powerful she was in Infinity War, when she was able to repel Thanos while simultaneously destroying Vision's Mind Stone. So it stands to reason that Wanda would have been able to single-handedly whoop Thanos into oblivion, had he not called in cover fire from above.
It's mentioned in several stories that Thanos' biggest weakness is himself. As shown in this dialog with Adam Warlock, Thanos loses because he doesn't feel worthy of the win.
As Thanos arrived, Vision convinced the devastated Wanda Maximoff to destroy the Mind Stone, killing him, only for Thanos to use the Time Stone to then resurrect Vision and rip the stone from his head, killing him for a second time as Thanos claimed his victory.
Even though Ultron is one of the most difficult opponents the Avengers have ever faced, he simply can't measure up to the godlike being that is Thanos. Even if Thanos doesn't have The Infinity gauntlet at his disposal, he is still stronger, more durable, and has more diverse abilities at his disposal.
In a one-on-one fight, Thanos could easily break through Ultron's armored body and destroy him. Ultron's weaponry combine Stark and Chitauri technology, and while his energy blasts are deadly, they still wouldn't be enough to defeat Thanos.
Even if Mjolnir was taken away from him, Thor is many times faster and stronger. If Vision attempts his standard move - phasing through an opponent and becoming solid - it's more than likely Thor will just rip through his opponent.
Thanos didn't lift Mjolnir, Captain America did
With Mjolnir's worthiness enchantment resulted in Thor being able to lift the hammer only if he is considered to be worthy, but likewise, the enchantment is not discriminatory in nature, and anyone who is deemed worthy is able to lift the hammer.
Hawkeye. On numerous occasions in the comics, Clint Barton has said he's just a regular guy with a bow and arrow. Unfortunately, his lack of power usually leads to him suffering injuries regularly and has led to fans deeming him the weakest member of the Avengers.
The strongest, most logical theory why Vision can lift it with relative easy is due to the fact he is created with an Infinity Stone – the one found within the gem of Loki's scepter.
Vision has added abilities because of the mind stone he wields and he would be able to outlast Aquaman. Vision's AI brain would give him faster reflexes than Aquaman. By using the concentrated solar blasts he has from the infinity stone, Vision would have more tools in his arsenal to beat the Justice League hero.
Wanda Maximoff has never truly been defeated, only "losing" to the combined forces of Doctor Strange, Wong, and America Chavez after realizing the error in her ways. For a time, Wanda posed the greatest threat to the Multiverse, going on a violent rampage on Earth-838.
Original Doctor Strange was more powerful than original Wanda. Original Doctor Strange, a. k. a, classic doctor strange could do literally anything and was one of the most powerful beings in Marvel.
The polished fighting style of Thanos proved too much for Hulk and his overall brutality and savagery.
Of the Avengers who can beat Scarlet Witch, Vision is one of the strongest contenders. With an Android created using the Mind Stone, Vision possesses a vast array of abilities that could potentially match Scarlet Witch's reality-warping powers.