I would like to talk about how the players themselves will treat eachother in their respective factions. Much is known about the so-called "higher" and "lesser" races in the Elder Scrolls lore.

The Altmer(High Elves) are the best example of a so-called "higher" race. They think they are the ultimate soloution of Tamriel and look upon men and beasts as lesser beings, and not worthy of them.

The lesser races are often considered to be the beast races: Khajiits and Argonians most looked down upon. Especially by the Dunmer(Dark Elves). The Orcs and to a certain degree the Bosmer(Wood Elf) have also been seen as inferior to men and High Elves.

My question to all of you is how will this affect how PLAYERS are talking to eachother in-game?
Will it affect who's in charge in the different groups? How will it affect cooperation in building and combat?
Do you think unintentionally/intentionally a Dunmer will treat an Argonian badly? Or an Argonian maybe will be less inclined to take orders from a Dunmer?
In the Aldmeri Dominion would it be a problem that the Thalmor are kind of the unquestionable leaders of the faction? How will an Altmer react to a Bosmer and Khajiit character? How will Khajiits and Bosmers behave when talking to an Altmer PC?

I want to play a Khajiit. My character don't like being treated like a slave(For the record: I personally dont like it either). How will I react to a Altmer char? And how will a Altmer char react to me?
These kind of reactions between players depends of course on how well the players are familiar to the Elder Scrolls lore and if the act upon it.

A thousand years later and 100 years before the events in the game Skyrim, the Thalmor claimed that they made the moons Masser and Secunda reappear after they vanished. Since the Khajiits are very connected to the moons they saw this as a kind of divine intervention and Elsweyr eventually left the empire and became part of the Aldmeri Dominion. So this happens just before Skyrim.
(The Aldmeri faction in ESO is in fact a striking similarity to the Aldmeri Dominion in Skyrim. Same races)

So culturally there is not far-fetched that a Khajiit will look upon the doing of an Altmer as something divine, and therein hold the Altmer in some regard. These could also happen the other way around. Or it could create aggression on both sides. In the Ebonheart pact the Nords dont like the Dunmer, the Dunmer dont like the Argonians, and the Argonians dont like the Dunmer. So here its different.

Do you think the possible aggression between races will be a challenge in the factions, or do you think this will make the factions even stronger when players try to rise above their differences?

Edit: Sorry about the topic title. A bit confusing.

Not at all...

Once players get in game, they'll just think of themselves and other players as members of the same faction, and so they'll be a sense of in-faction camaraderie, but other than that, this won't come into play at all unless people are intentionally role-playing. At the end of the day, people get really into the game, but at the same time, they remember that it's just a game.