TLDR: The Ebonheart Pact fits just fine into the Lore IMO.
Some points to remember.
-We do not know the true details of the Alliances yet, but we do know some things. This is at best educated Speculation.
-Remember not all the Dunmer are racist slave owners and not all the Nords are Mer killing beer swilling barbarian warriors. In fact most are not that way at all. Same with the other races. Not all Argonians are slaves, and few are truly savage like anyone would think. For instance it is supposedly a common trait for Argonians to be skilled at Illusion magic but there are likely several exceptions to that generalization.
-Do not underestimate practicality. You would be very surprised by what normal people will turn to when they are desperate enough.
-No one else including me truly knows how people in Tamriel thought back in 2nd Era as we have little to base it off of.
The Nords have worked with the Dunmer before when under an overbearing threat. The attempted invasion of Tamriel by the Kamal from Akavir that was defeated by the Underking(Ysmir Wulfarth) and Almalexia.
According to the Interview video with Paul Sage, The Ebonheart formed in the following way though he was kind of winging it so I am making some assumptions. Here is me paraphrasing. The Nords and Dunmer were under attack and were losing territory. The Nords felt especially beleaguered so they turned to the Dunmer for help and sought an Alliance. The Dunmer accepted and then both groups asked the Argonians for aid who accepted so they would supposedly get better treatment from the Dunmer. This is a somewhat unstable alliance that supposedly formed AFTER the other factions formed.
With the growing pressure from the newly formed Aldmeri Dominion and Daggerfall Covenant, as well as the chaos brewing in Cyrodiil with their Imperial kin falling under the the machinations of a Masterful Necromancer, Mannimarco, and a Daedric Prince, Molag Bal. In desperation the Nords would have little choice in terms of allies if the Daggerfall Covenant wasn't interested or only wanted their surrender. This is a point for speculation, why would the Nords have been turned from the Covenant? There may be some answers in the form of old grudges between the Nords, Bretons and Redguards. The Nords may not get along famously with the Dunmer but there is nothing to suggest they would not work together begrudgingly. There is also precedent for them working together against a bigger threat, though admittedly nothing on this scale.
It is not really that incredulous that an Alliance would form. Might I add that I am a hardcoe Nord and Dunmer fan that is well aware of how much we know of how the Nords and Dunmer viewed one another throughout their histories together. However even recent views, when taken into account, are promising. The Nords took in the Dunmer refugees and did not interfere with their claimant of Solstheim in the 4th Era. They even let them have residency in their traditional capitol Windhelm. A veritable Hallmark of Nordic Culture and a place where the conflicts of the Mer and Men of the past is likely a very present thought in the minds of both groups given the History of the Area.
The more recent views of the Nords as true Mer haters by fans in Skyrim is likely mostly due to the recent events such the Thalmor as well as the ancient events, like the whole thing with the Falmer. Even that has events that excuse the Nords hatred of Mer, initially they got along with the Falmer but then the Eye of Magnus was discovered and the Night of Tears happened. They even respectfully buried the leader of the Falmer, the Snow Prince, in a gesture of respect. My point being that the Nords are not completely ignorant mer haters on principle.
So given that, I think an alliance between the two is easily within the bounds of the Lore and not far fetched at all.
Now here's where it is touchy ground. The Argonians. We simply need more info than we have. But going off what I know I will try to explain.
As far as I know at the time the MMO is taking place is a rather bad time for Black Marsh. There are hordes of Bandits and Pirates everywhere and Imperial Warlords are scattered throughout the province ruling the Second Empire's old holdings. How organized the Argonians are at this point is unknown. There was a major spike in slaves at this time. We know the Argonians sold their own into slavery and similar to the various rival tribes in Africa most of the actual slave nabbing was done by locals like the Archeins. Here is some interesting stuff.
http://www.uesp.net/wiki/Lore:Pocket_Guide_to_the_Empire,_3rd_Edition/Argonia
In the chaos of the Second Era, banditry returned to Black Marsh in force. Slave traders from Morrowind were freer than ever to exploit their southern neighbor, and entire tribes of Argonians were dragged in chains to the Dunmer land. Former Imperial officials founded warlord dynasties which earned a reputation for tyranny even in that dark time.
Whether the terrible Knahaten Flu arose from natural causes, or was created by an Argonian shaman in retaliation for his people's oppression, is still a matter of debate. But its result was clear. The plague began in Stormhold in 2E 560, and quickly spread to every corner of Black Marsh, killing all those not of reptilian stock. For over forty years, it held the Province in its grip, decimating entire cultures (notably, the Kothringi) and driving outsiders from the land.
Whether the terrible Knahaten Flu arose from natural causes, or was created by an Argonian shaman in retaliation for his people's oppression, is still a matter of debate. But its result was clear. The plague began in Stormhold in 2E 560, and quickly spread to every corner of Black Marsh, killing all those not of reptilian stock. For over forty years, it held the Province in its grip, decimating entire cultures (notably, the Kothringi) and driving outsiders from the land.
Archeins: During the era when other races tried to put plantations in Argonia, Archeins were very powerful, and made fortunes by selling other Argonians into slavery. Since the other races realized Argonia is unfit for plantations, they have gone bankrupt.
This could mean the Archeins are in control and are on very friendly terms with the Dunmer for the purpose of selling slaves. I think that Black Marsh is a bit of a Kleptocracy during this period and even until later in the 3rd Era. Of interest is the http://www.uesp.net/wiki/Lore:The_Argonian_Account
Now if this is the case or even if it is not, the Argonians need protection from the Dunmer slaving interests, Bandits, Imperial Warlords and the growing threats of the other powers as well as the whole Molag Bal and Mannimarco thing with the Imperials The way they are getting their protection from the Dunmer might be that they intend for this alliance to improve the relations with the Dunmer and possibly convince the Dunmer they are not lesser beings. It also is worth mentioning that the Dunmer and Nords supposedly approached the Argonians after working out their own deal if what Paul Sage has said was accurate.
When two strong peoples that consider your people to be inferior ask for your help when you need it, you kind of feel a need to prove yourself and them wrong. Just working a theory here. It is also possible the Hist, Greybeards and the Tribunal had some fun kind of commute and that netted them a necessary if unstable alliance with old hatreds by nature being a common problem and those problems commonly rearing their ugly little heads.
Alright whoever wants to explain the Aldmeri Dominion and Daggerfall Covenant go ahead. I think the Ebonheart one was the most controversial one.
Anyone have anything to add to this big 'ole wall of text?