Ally is not a precisely-defined term in 5e D&D.

You are unfortunately dependent on the normal English meaning of the word, and thus it is largely the DM's ruling as to whether or not two creatures count as allies or not on a case by case basis. The Oxford English Dictionary defines an ally (in this sense of the word) as:

A person or organization that cooperates with or helps another in a particular activity.

Personally, I would tend to rule that creatures are allies if they are co-operating together and would both agree that they are allies at that moment, and so abilities that affect allies do not affect creatures that you do not currently regard as allies or that do not regard you as an ally.

This does allow for alliances of convenience - two creatures who are entirely unfamiliar to each other but nonetheless find their lots thrown in together could treat each other as allies if they like. Say, for instance, two prisoners who do not know each other but are thrown into the arena together to face a beast - if they're willing to work together, they can be allies.

It also allows for deceptive alliances; say in the example of the doppelganger who has infiltrated the party. They may ultimately plan to betray the other members, but it's perfectly acceptable for them to consider them as allies and thus get the benefit of allied abilities up until the moment they turn upon them.

Making it simple

If the precise classification of who is and isn't an ally ends up taking up too much table time or prompts arguments, then as a house rule you could simplify such targeting rules by replacing references to "ally" with "willing creature you choose". There are a probably a few edge cases where this might cause a notable change in effect resolution, but it seems to me that in most circumstances it would result in targeting which was consistent with the intention of the ability.

Probably yes

Based on this Sageadvice article asking different question about the interaction of fear spell and Aura of Conquest, Jeremy Crawford answers imply that the fear spell and Aura of Conquest do work together; Aura of Conquest reduces the speed of a creature affected by fear you've cast to 0.

Q: if a creature is under the fear spell (must use action to dash) but in the aura of conquest (reduces speed to 0) do they waste there action to dash with 0 speed or at that point can they use there action as normal? Thank you for any advice

A: If you're under the effect of the fear spell yet have nowhere to move, you can use your action as you like. (That's what "unless there is nowhere to move" is getting at in the spell's text.)

However, as you've correctly noted, the fear spell does not explicitly state the creature is frightened of you, but as a DM I treat "the source is you" and "frightened of you" as the same, because it is what the players would expect and the simplest interpretation of it.

Your DM might rule otherwise, and it is correct too, since the affected creature does not frightened of you, but its own worst fear, projected by you. Technically, they are not seeing and fearing you, but whatever its own worst fear.