Hoo boy, we're asking to counter Death Battle? I mean, I like them, but they set up some easy hits sometimes...
There's really no question that Awakened Zero is the strongest Zero, at least as far as Wily's designs (you could argue Absolute as post-dating that, I suppose). He is the endpoint of Wily's whole rivalry agenda with X. Genmu Zero is also regularly shown to be Zero's ultimate attack in crossovers and such (Project X Zone strongly implies that it is Zero's answer to X's ability to use ki attacks like the Hadouken). Death Battle most likely ignores Awakened Zero because it is triggered by viral exposure and not of Zero's own free will, but I do think they goofed up in that they regularly consider merchandizing outside of the core canon to determine a character's best potential (for example, using manga Quick Man for speed comparisons), yet ignore Zero's use of Genmu Zero in Project X Zone and a variant of it in Marvel Vs. Capcom 3.
For X, I suppose there's some debate, since many of his forms are optimized for different circumstances. For raw firepower, it's hard to argue with the flying fortress that is Command Mission's Ultimate Armor. But in terms of gameplay mechanics I think the Shadow Armor deserves an honorable mention; with the right Power-Up Part loadout it is quite the engine of destruction (most notably Overdrive which shreds most bosses, and Ultimate Buster for constant use of the charged saber). If we're comparing the various Nova Strike's specifically, I would rank X6's stronger than X8's. Try it on High Max, it positively rips him apart. X8's Nova Strike is also far more restrictive given how long it takes to charge.
Sigma is anyone's guess. I agree that Final Sigma W and Belial Sigma are the two strongest contenders. Personally I lean towards the latter. Death Battle's lacking of its use is probably just an animation decision; the simple reality is that he was matched against Ultron and that battle was always going to be sheer speculation as to which one is more likely to hack the other. I believe they decided that incorrectly; Ultron obviously has more brute force to apply to a ridiculously large scale, but the Sigma Virus is known specifically to attack the "suffering circuit," a moral center which endlessly debates the value of organic and artificial life, according to Mega Man Zero Official Complete Works. "Moral value of life" is a concept in which Ultron is known to struggle, as DB itself notes that he self-destructed from merely reading a text which stated not to kill, and frequently falls to other computer viruses.
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