Just for argument's sake: The first game in the series was called "Arena" because Tamriel was so riven by warfare that the land was essentially though of as one massive fighting pit. For every horrible, traumatic injustice the lore has spotlighted so far (the sacking of Orsinium, slavery of Argonians), there could be dozens of others not encountered yet which would make *any* conceivable combination of races into a faction equally is implausible. The Khajiit and Bosmer clashes driven by border disputes and deep-seated cultural clashing is one that comes to mind, but the Bosmer have had bloody wars with the Bretons in the past, too, and the whole (stated) impetus for the creation of the Trans-Niben was Imperial desire to keep Argonians and Khajiit from constantly killing each other (according to Oblivion, anyway). In the North, the Nords have often been considered super-aggressive, with an innate drive for heroism and bloodshed which they have imposed on the Dunmer in their quest for The First Empire, and the Bretons and Redguards in their quest to bring back the old dream of such an empire. There's conflict with the Reachmen, and with the Orcs, both of which have their own interests and natural aggressive dispositions. Why should we imagine that two super-aggressive races are probably "more friendly" than other imagined alliances just because we haven't yet seen their conflict in a game?

To be fair, I think that sometimes (moreso early on) ESO misses some of the TES story-telling nuance: its harder to swallow the idea that most Dunmer were so removed from the nords that they legitimately believed nords were wind-demons when all they needed all along was Rigurt the Brash to bumble along and spout some nonsense about mead, but the major point is that given the tone of Tamriel, if there are two races/provinces that haven't been at war yet or seem like natural friends, who haven't committed atrocities against each other, its only because they haven't gotten around to telling that story yet.

As for alliances, I think that its already played-out very well in this discussion, everyone has good points, and based strictly on the OP's question it could be hard to justify. Though if I had creative freedom to re-envision the war, what I'd love to do is bring it more in line with what the lore says about this period of time: specifically that the Interregnum, a period of several hundred years, was characterised by rapidly shifting alliances. Its interesting to see people talking about which of these 3 factions will win in the end, when none of them seem likely to last any significant period of time, and will probably be rather insignificant in the grand scheme of the period.

What I think would be an interesting alternative is for something like what they did with Ravnica in MtG- where each colour was represented by multiple factions, each of which would be defined by their alliance with another colour. In this case, colour could be replaced by race, or province. Instead of having it that most Bretons- who's defining characteristic is their fractiousness and factionalism- simply get behind Emeric, I'd have two possibilities: The traditional Daggerfall Covenant, and, say, The Colovian Compact with Nords, Imperials and Bretons who can't swallow bedding up with two factions they have fought against for thousands of years. By lore, there's this interesting friction between Daggerfall and Wayrest, and this could be proxy for the alliance alternatives you could choose. Alternatively, "high medieval" Illiac Daggerfall and Wayrest might have very differing alliance preferences to "dark ages" Evermore and Jehanna.

I think in such a way, you could come up with interesting factions and alternatives for alliances you find hard to believe, and it would put more of a lore spotlight on this incorrect notion that each of the factions are monolithic and perfectly aligned, despite their pasts.

Mechanically, it would fly in the face of what we've had for the past 8 or so years, but arguably the innate equilibrium that 3 factions were supposed to bring to objective-based gameplay in Cyrodiil doesn't really reflect the reality anyway. But also, in the spirit of the instability of the period, perhaps allowing people to re-choose their faction after every (1-month) campaign could be a soft counter towards being locked into some fringe faction that no-one's playing.

But for me, I think the 3BW has kind of played out its tale. It was a great story 8 years ago, but when the tone of the rest of the story can be reassessed with every new chapter to meet the needs of changing times and an evolving audience, it feels like its being left behind as a stale relic. I like questions like this, and hope that they can inspire more thought about what could be.