I was actually considering making this btw.
Now to get into it. I'm gonna start with non-hax abilities since I already detailed why AP is more or less equal
Both of them have energy manipulation and absorption (through similar means as well, since Zero's Saber can absorb energy with certain elves, and Thor's hammer can as well (it's what grants his power nullification, similarly) as well as intangibility They both have statistics amplification (Zero through Cyber Elves and his forms (the former of which is exponential in some cases, incremental in others), Thor via warriors madness and Megingjord). They also share elemental manipulation, but Thor's a bit more versatile. Their roughly comparable in these regards
They actually seem similar in a lot of ways, but I'm going to side with Zero with regards to Statistic Amplification. His statistics amplification (ie, doubling his durability) is permanent, not temporary, and he can increase more than just his power (he can increase speed and durability)
This is just their physical abilities (mostly), and while I think Zero is slightly more effective here overall, Thor also has flight to consider. Additionally, both have Regen, but Zero's is better since his regen should be comparable to Copy X (and superior via Cyber Elves) who has high-low regen vs Thor's Low to Mid-low regen. Stamina is more or less irrelevent, since both have virtually no limit of it as long as they aren't badly harmed
If neither had hax or there wasn't a difference in combative effectiveness (I'll go into that later), this would be inconclusive for me, and the AP difference is pretty marginal. In the regard of non-hax abilities, they're more or less equal.
Before I continue, there's some things I wanna bring up before someone else does because Zero is a machine.
1) Thor's magnetism would not work on Zero, he is barely even affected by massive amounts of magnetism in Z4
2) Electricity wouldn't short out Zero, he tanks electricity all the time
Now we move on to hax
This area is similarly very close, and both share a lot of powers, but this is a bit easier to decide. Zero takes this category. He has almost all of the same hax powers (the one's he doesn't being irrelevent since Zero has dealth with illusion creation, and Zero isn't dumb enough to get into a BFR Portal nor is it in character for Thor, and lastly, Thor hardly ever, IF EVER, uses intangibility in a fight, much less with someone his rough equal), and a few more including time stop (Thor no longer has it), status effect inducement (namely to weaken, freeze or otherwise debilitate Thor), absolute zero, intangible doppelgangers, possibly mind manipulation (debatable, but if he CAN, I dunno if Thor could resist it, since), biological manipulation (specifically transmutation (IE, Turning Thor into an E-Crystal)) all give him a decisive edge over Thor's 3 abilities over Zero
But what REALLY gives Zero the edge here, is resistances. He resists everything his opponent is bringing to the table, even former abilities, and attack reflection/absorption cancels out, since both use them. Meanwhile, Thor's resistances are dubious (as in, possibly) or nonexistent (status inducement), giving Zero a decided advantage.
Lastly, it also helps that Zero uses his hax far more often in-character than Thor, who prefers physical combat
Zero gets the edge in his hax abilities.
Lastly, there's their combative effectiveness (namely, their skill and general approach to combat). I feel like this is the true deciding factor, as they're so close otherwise that I think this fight would be really inconclusive if I didn't go into this.
Skill wise, these two are very close, having hundreds of years of combat experience with tons of weapons against tons of adversaries. They are both also surprisingly cunning when the situation calls for it. Were this a contest of pure, raw skill, I would, once again, say the results are inconclusive. Though it is worth noting Zero carries most of his weapons while Thor just has Mjolnir, that really makes no difference to me.
However, in terms of mannerisms and approach to combat, Thor is at a SEVERE disadvantage. Thor tends to hold back against foes of earthly origins, he is extremely arrogant. Zero, by contrast, goes for the kill immediately and holds no high opinions or views of himself. He is just fighting for those he believes in.
Additionally, I feel that Thor's growing anger (He'd get angry over the course of the fight even without Warrior's Madness, as his frustration with fighting Zero would increase as time went on) would lead him to make a rash move that sends him off course or otherwise opens his defenses, leaving him open to dismemberment (which only Zero would be able to shrug off), decapitation, or a quick stab from Zero. And the reverse does not come into play as Zero is for the most part, completely stoic, Deadpan Snarker moments aside.
Therefore, after a truly epic duel, I give Zero the victory, roughly 6/10, though this is really close.