What a bump!
Actually, I managed to get a friend of mine mad/zzzing in contemplating this. The first thing I noticed was that the hps would probably have to be adjusted.
Argument 1 against hp adjustment: Warcraft characters can tank a lot of sword hits and spells - perhaps they are supernaturally endowed.
The cinematics tell a different story: that the in-game mechanics are just a user-friendly representation of what appears to be normal combat. To cite the most obvious example, Thrall lost his hammer in one strike against Mannaroth, while Grom killed the pit lord in one single blow.
Argument 2 against hp adjustment: don't make excuses about your failing game; be a man, not a wuss.
This isn't really an argument.
So the big question of course, is: what's the conversion factor? My initial basis of comparison was the one race present in both games: human. Specifically, the marine having 40hp, the footman around 420 (though it depends) leads to a convenient conversion factor of approximately 10x. Perhaps the WC units, being more used to the harsh wild, are more buff physically.
Other possible factors include the Hydralisk in the NE campaign (which suggests a conversion factor of somewhere around 14x, with the 10 explosive damage in SC converted first into 140 explosive damage in WC, then 70 normal damage - presumably this is a worst case scenario, as explosive does half damage against small units). All this makes precious little sense, and I'm going to presume it was just put in as a joke without much thought put into it.
Anyways, the natural assumption seems to be 10x, if only because it's easy to calculate. The "guns vs swords" stuff actuallly makes a bit of sense under this conversion. Swords and primitive rifles do about 1/4 the damage of advanced gauss shells, etc.
---
Once I realized this, the natural conclusion (which sent my friend mad/zzzzzing) followed. In WC scale, marines do 80 damage, while alliance humans would be lucky to do 20. Zerg could raise up swarms of zerglings (with 350hp) who could do 50 damage per melee strike. There exists a race whose basic character has 1000hp and 600 plasma shields, and does 160 damage per melee shot. Battlecruisers have 5000hp and do 250 damage per shot, along with a 2600 damage Yamato cannon. Siege tanks have 1500 hp and do 700 explosive AOE damage in siege mode. Ultralisks have 4000hp and do 200 damage each. Psionic storms do 1100 damage to non-buildings over 4 seconds. Not only are hps comparable or higher, but SC units do more damage (which makes sense, as they're using futuristic weaponry).
---
That's the easy part. Clearly, SC units dominate WC units in terms of damage and hp. However, you then have to compare the relative magics of the two games.
This gets much harder because WC3 has many different subgames with different damage levels. One hero in X Hero Siege, for instance, would probably be able to uberpwn everything (as well as Archimonde, assuming they can get past divine armor). If you are limited to the stuff that appears in the campaign (and the battle.net stats), the magic damages, while not that weak, are not really that strong - at least, not strong enough to supposedly turn the tide. Lv 3 Chain lightning, for instance, does 180 damage. It hurts, but a medic will heal that off in 10 seconds. Level 3 Death Coil? 300 damage per coil. Lv 3 Flame strike does something like 400 damage in an area. Okay, but not really tide-turning. Priestess with Starfall - now we're getting there, 30 waves of 50 damage each for a raw total of 1500 damage. If you have a lot of Priestesses, it might start to even the odds.
---
Being pessimistic is pretty boring, so let's come up with the real questions of interest.
1) Divine Shield vs Nuclear Launch - HEHE
2) Spawn broodling vs spell immunity - This was mentioned before, I believe. For the sake of argument, let's say broodling doesn't work.
3) Shades vs cloak detection - Since shades can be killed by some guy with a sword, it seems likely there's something there that can be detected. However, for the sake of argument, let's say shades, owls, etc are undetectable.
4) Divine armor vs Yamato cannon - I guess this question actually applies to weapons in general, and it doesn't help that they're very vague on what divine/chaos stuff is. Because of the vagueness involved, this question remains open.
5) Feedback vs mana - Now this is an interesting one. For those who don't remember, Feedback (the Dark Archon ability) combusts all energy and deals 1/10 (SC/WC) damage per energy point. (Much better than spell breaker, amirite.) This can really open Pandora's box. For example, if 1 mana = 1 energy, Feedback will almost certainly OHKO anyone who has mana. If 10 mana = 1 energy, the hero had damned well better be sure to use up their mana quickly, or be severely damaged. However, because no conversion rate is hinted at, this question remains open.
6) Mana vs EMP Shockwave - I'm tempted to say EMP wins this one. Sorry, guys.
7) Zerg evolutionary virus vs undead plague - This is very, very interesting (one is basically a copy of the other, after all) because it's a question of "just who will infest who?" On the one hand is one pinnacle of evolution under the Xel'Naga, while on the other the pinnacle of corruption under Ner'zhul. I anticipate months of attempted infestation on both sides, and whoever wins, it'd be an awesome battle on the microscopic level.
8) Naga vs Xel'Naga - with artifacts that can bring about "the end... of all things"? I don't think so.
---
Storyline:
It'd probably be something about: The Zerg detect a psionic entity remarkably similar to theirs', and decide to infest the Undead, believing that they could be used to upgrade the zerg evolutionary virus itself. After months of spying via a goblin interface, Infested Kerrigan warps all her forces to Azeroth. The Lich King, however, has other plans for her brood.
Following her, the Terran Dominion is surprised to discover an offshoot of their own race, struggling for existance. After a battlecruiser hastily eliminates a small force of Undead croaching upon Stormwind, the native humans quickly realize they may have found an immensely powerful ally.
The Protoss, determined to prevent Kerrigan gaining even greater power by infesting the Scourge, have also followed in their wake. Meanwhile, a Protoss scholar begins to wonder what connection this Burning Legion might have with the Xel'naga vow to "end all things".
All in all, the Legion itself has lay immensely quiet on this land. But the new arrivals do not have time to worry about them yet. First, they must find a way to supply themselves with minerals and vespene gas...