Doom could win and here's why (remember, I am quite a big Who fan)
Time works differently in the Marvel U. You can't mess with history there, whatever you do, it'll just create another reality. The Doc is used to using time-travel to fix problems but even if he went back in time to "fix" Vic he would just create another world where Vic was "fixed". The Doom he has to go up against is still waiting. Also, Kang is one of the most complex "time" characters, messing with Marvel timespace (which is much more advanced than Who timespace) since his first appereance, to the point where there are three versions of him inhabiting current Marvel but from different time periods.
Now, thing is, Doom can travel between realities as well, not only time, something that the Doc has difficulty with (though that's not an intelectual problem, it's just something which has to do with is U). Also, the biggest ace up Doom's sleve is magic. Remember, Who doesn't really classify magic as "magic" whereas Marvel has a Hell, a Heaven a sorcerer supreme and all that. Doc may have a ton of tech-savvy but Doom is second in line for Sorcerer Supreme and has tangled with the likes of Mephisto, Dormammu, Shuma Gorath, which are people who are waaaay above the Doc's paygrade.
So, bearing that in mind I'll give it Doom. Removing all of his scientific feats his magical feats are still enough to give him the edge. Remember, this is the guy who stole the Beyonder's powers, the Surfer's AND went up against Galactus. He didn't trick him to be good or any fot he Doc's techniques, he straight up stole his powers. And the Beyonder is a Mutant/Inhuman who was also an uninhabited universe who decided to start messing with reality. Really, the Beyonder is living, breathing universe that has Infinity-Gauntlet level powers and Doom still went against him. Eventually he lost but that's because he's a villain. Same goes for Doc who always wins because he's the star of the show. Most of the time the plot relies heavily on Deus-Ex machinas or PIS.
Also, for the guys who don't know anything about the Sorcerer Supreme, Classic Strange was deemed way too powerful by Eternity and the Living Tribunal. So yeah, Doom is second in line for that position.
Dr. Doom would win, his armor is impervious to anything Doc Who could do to him and Doctor Who doesn't kill, Doom would shoot the 11th doc and move on. Besides Doom has his own time machine, he doesn't need the Tardis.