So Alessia made up the imperial pantheon for political reasons and it seems to be the true faith when its mixed with other cultures. For example the nordic pantheon said that Alduin was a god, now they call him the first born of Akatosh and that seems to be true, it makes me wonder if Alessia wasn't just acting for political reasons, but for the gods themselves, and it is a mystery weather she knew it or not.

Alessia "made up" the current cyrodilic pantheon but they are certainly real gods. Belief shapes a lot of things in TES, the gods foremost amongst them.

To put it over-simply, imperial culture is the most wide-spread on Tamriel therefore the Gods seem imperialized. The gods are shaped by mortal perception.

Also, they call him Akatosh to be convenient. To dragons, he is Borhamu.

Everything is true to somebody in a world made of myth.

Colossus, is it "Borhamu" or "Bormahu?" I thought it was the latter, and see below.

"Akatosh" was the name that humans seem to have used for Auriel, the elven god who is counterpart to, and at one time was, Alduin. There was a bit of a big ole Dragon Break that may have accelerated the split when Alessia re-wrote the traits of Akatosh and caused him to split off from at least one of the other two.

The reason, as far as I can tell, that Dragons don't recall a time when their "father," (someone know what the -u suffix means in Dragon Language, because "Bormah" is their word for father) but humans can is because they are so linked to time. Paarthurnax says that Dragons are somehow "vulnerable" to anomalies. So, for example, a dragon would also not remember a timeline where Vivec was mortal. But humans are more rooted in space (Lorkhanic) so they remember a time when Alduin was Akatosh and Vivec was just an elven hermaphrodite warrior-poet.

I sort of get this vibe reading about the Dragon Cult and how it was benevolent until it reached Tamriel that perhaps this split of Akatosh and Alduin was only Tamriel-wide. Atmorans acknowledged the kalpa cycle as a natural process if a bit of a bummer, so Alduin was a god without a moral tag. Then they, and Alduin, come to Tamriel and are changed because, when Akatosh was retroactively altered by belief, so too were his counterparts.

Basically, go read Terry Pratchett's Small Gods and Pyramids, then take away the funny.

Because the Empire is wide-spread, and the best way to unite an Empire is to have it all to share the same beliefs.

One could also say the Daedra are even more true, since they actually appear frequently to mortals. The gods do seem to be shaped by perception, as pointed out above, and maybe it's the same thing.

Expanding on my earlier point. If you get two groups large enough worshipping the same god with different perceptions of it, you end up with aspects.

Aspects happen regardless, because traits are valued more, location from location (time or space).

It seems they are truer, because we've been the Empire-friendly agent for so long; and the games' developers present a very lethargic, stereotypical Tamriel.

As below, so above.

Notice that it's called a "well researched synthesis." It's not an accident that it appears to be true; it's true because she made a determined effort to find out what the truth was.

It's not the whole truth, but it is one truth. And, as others have mentioned, people believing it's true makes it even truer.

So if the dragons are so rooted in Time that they are susceptible to time anomalies, what sort of anomalies do men and mer miss? Deleted lands? Various realms? Multiple universes?

Yes, yes, and yes. Read "Where were you when the Dragon Broke?"

Deleted lands. They only know that there were lands present in the first place because Pelinal mentioned that he unmade them by accident. Much like how if you told Paarthurnax that there was a different imeline he would "know" of it, but likely not believe it or have any memories of it having been. Alessia, say, would maybe remember the lands Pelinal unmade because she was Dragonborn (eventually) and therefore in the between place of a hero, but her more mundane generals and the Ayleids would not unless a dragon or a god happened to have seen them and knew they had been there.