Interesting match up, I wanted to make it ever since Ultron was upgraded to Low 1-C.
So, first of all, after the new revision now Infinity Ultron scales far higher in AP, which gives him the advantage on that, and his blasts as mentioned before can atomize the target easily. This gives Ultron a huge advantage in a fight since both his physical and his ranged attacks will kill the Doomguy.
On top of this, he also can use other powerful haxes if he loses control of the situation, and Doomguy doesn't seem to resist many of those.
Doomguy definitely have the skill advantage since he is a far more expirienced fighter that took head on armies of Demons alone, and this will allow him to avoid many attacks and possibly even hit Ultron a couple of times. This, along side the powerups, might give him some chances in the beginning, but the moment Infinity Ultron decide to use his huge AoE, which are at least planetary up to galactic in range, he will have no chances of avoiding and he will be destroyed.
Now, regarding the Fate Hax, it have it's limitations. It allows Doomguy to "eventually" come back, but he can still be reduced in a condition in which he can't do anything and he can be incapped. If he is atomized or even if his physical body is destroyed by AP, he wont be able to continue fighting since he doesn't have the regeneration necessary to back that up, and even if we want to say that he will be able to "eventually" come back thanks to Fate Hax, the time frame will be very long, longer than the 24h required for Infinity Ultron to win the match.
Overall, Doomguy have a huge skill advantage, which however is not enough to overcome the many advantages Infinity Ultron have overall. So, I will vote Infinity Ultron.