Aaaand another wall of text incoming! * Loud booing can be heard *
I agree with Cal on the Hadouken and Shoryuken (and by extension X3 Z-Saber and X8 Nova Strike) OHK feeling too much like game mechanics, we can take them as being powerful attacks but by being easter eggs and all their power could be easily taken as "rewarding the player with an OP move for kicks". Being usable is more justified because the Hadouken gets acknowledged in other of X appearances, in X8 he has a shoryuken like move, the Nova Strike is a staple super move for him. His X3 Z-Saber (where he sends a blade beam that takes 3/4 of bosses health and obliterates every other enemy) is kinda contradicted by X6 where he can use it but much more clumsily than Zero whose only move with such power is the Genmu Zero a secret skill he can only use as a Maverick. Zero is also clearly superior to X in close combat and swordsmanship, so X pulling a move like that right away after getting the saber in X3 comes as iffy, when even with upgrades in X6 he still falls behind Zero with it.
And it's true, Ganon needs just his soul to come back, Meta Cooler can be destroyed if his body is gone. Reason why only the Master Sword or Zelda pulling some trick are the only things to do the job, and even then they don't stick.
Link can also deflect powerful magic with his almighty bug catching web, BTW. Ask poor Aghanim =P
Well, in X8 several of X's moves can destroy barriers and break guards.
The Regenerationn I mentioned for X is the one from the Mother Elf, not his manga self (we're using composites from the games). The same one that kept reactivating and made Omega so unkillable until Zero woke up and took the Dark Elf from him. Link can negate it with the Master Sword and the Silver Arrows, but he does need to hit X with one of them first, doesn't he.
Many of X's AoE are energy attacks; the Falcon Armor Giga Crush, charged Ray Splasher is a rain of energy, the charged Gravity Well (normal is also a high gravity zone that atracts and crushes) and Squeeze Bomb can be an AoE black hole. Charged Frost Tower, Gel Shaver are AoE Absolute Zero attack (and charged Ice Burst creates icicles wherever X dashes through, while charged Drift Diamond creates a freezing barrier around X). Guard Shell creates "drones" that shoot towards the target from four different directions, Metal Anchor creates a rain of Storm Eagle metallic statues. Homing attacks also help such as charged Wind Cutter and Homing Torpedo. Sonic Slicer, Shadow Runner and Boomerang Cutter are blade AoE attacks.
Actually if we could pile up every defensive gear for both characters, both X and Link would become absurdly unkillable. Link has a gazillion tunics and rings, X has 12 armors, each that halves damage without counting chips and parts. Armors alone could reduce damage by x4096 and with the X Drive it would either be x8192 if you apply it to the final number or even more applied to each armor individually... which is completely ridiculous as neither would even scratch the other. From what I got, with composites is essentially allowing them to use all their different abilities and items and be at the best condition displayed in what's being used, not really repeating an ability if he is already using it.
Reason while I am so stubborn with stamina is because how good each of the two's defense is. Getting openings would be hard, and none have a weak point to inflict huge damage nor to create space for a full assault, getting a good hit would be the best outcome. What I am trying to point is that Link can't be too aggresive or he'll get hit with a barrage, and while he can defend himself of the many projectiles, he has to go more on the defensive to do so. Don't forget X is more mobile: invisible, invincible dashing, multi air dash, hovering, flight, wall climbing and bouncing. He can drag things out, letting Link get close would be his doom but he can run away with other stuff like a Nova Strike, the Strike Chain (essentially his Hookshot) and several close ranged weapons that deadly on their own right may not manage to hurt Link, but can distract him for an opening to run off. Link will have trouble reaching X, but X has to be very defensive to pull it off. And let's not take it as Link being able to one shot X with anything at close range, X can take punishment, the issue is that he'd lose his regen, but Link would have to repeatedly attack to finish off X (same other way around, a single well placed shot form X won't put Link down). Unless, of course they use one of their OHKs and it hits, but that is hard already.
I don't know if Link has a regen as good as Ganondorf has. The regenation seemed to be more of an ability the King of Evil had that was improved by the triforce of power (makes sense given it amplifies his magic as well). I could be missing something, but if it's stated somewhere like Hyrule Historia or the games that the Triforce of Power grants such regen then it goes, otherwise we could be misatributing something that's actually Ganon's.
I had forgotten something important: X also has his Erupting Shining Fingahz voiced by Mark Gatha and everything, he can OHK anything with that based on his right hand of his burning blue. >_> <_< That should be canon, let me be a fanboy.
Lame jokes aside, wish I could speak for Cyber Elves themselves, but I never payed much attention to them in the Zero series (because they punished your mission rank for using them and I already sucked hard enough at the game). I tried looking up but all I found are the in-game descriptions which are pretty criptic.
EDIT: Holy freaking hell, I really outdid myself this time with the verbal diarreah. O_O