Originally posted by the ninjak
There is nothing Neo and Smith could do to Thanos whilst in the Matrix. Thanos undertook insane rigorous punishment whilst training himself venturing through the many different planes of reality in his earlier years.But the fact is his physical body can't die. He will just remain in the Matrix and keep fighting and evolving. The fact that he withstood Moondragon and Cosmos attacks handidly means he can withstand mental assaults on an insane scale.
I know Neo was the perfect equation born in human form. Born to die and try again. But Thanos even if it means BFR even if he is forced out of the Matrix he would simply destroy the physical world's machines surrounding him upon awakening killing the Matrix from the outside.
It's not a matter of Neo being more powerful than Thanos as Thanos is presented in the MU, it's a matter of, given the battlefield, Neo pretty much controls the terms of combat. In the Matrix reality, while Thanos/Bor would still exhibit the abilities they do in the MU, they would be translated as virtual representations, and as such, be within the ability of Neo and Smith to manipulate (as they would just be code, not their physical selves). It's the homefield advantage, not a matter of who is more powerful, ability for ability. Neo would know everything Thanos was about to do before he did it, and could simply gesture to stop it, or just move out of the way. He could also overwrite Thanos' virtual representation. Thano's 'real world' physical durability is a non-factor. In the Matrix he's just code with a superhuman ability set.
Also, the battle takes place inside the Matrix so the other points, while valid, are moot given the battle stips.