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I am rather confused on what is the Time Dragon's agenda. On one hand, we have Auri-El, the God-king of the elves, on the other hand, there is Akatosh, the ally of the men and patron of their empire.
The two are definitely the same, since "Akatosh" was created by Alessia by renaming/twisting Auri-El, and there is lot of evidence he really did contribute to the Ayleids' downfall (Amulet of kings was shown to really contain his power, Umaril did not exclude him from his quest for vengeance etc.).
Why did he abandon his loyal worshipers and subjects for sake of men, who are usually associated more with Lorkhan, not exactly his friend?

To add to your confusion here's an excerpt from "Mysterious Akavir":

'Ka Po' Tun is the "Tiger-Dragon's Empire". The cat-folk here are ruled by the divine Tosh Raka, the Tiger-Dragon. [...] Since that time the cat-folk have tried to become the Dragons. Tosh Raka is the first to succeed. He is the largest Dragon in the world, orange and black, and he has very many new ideas.

"First," Tosh Raka says, "is that we kill all the vampire snakes." Then the Tiger-Dragon Emperor wants to invade Tamriel.'

It's been suggested before that Tosh Raka is a play on words on AkaTosh, i.e. that's he's probably an avatar of the Time Dragon. And he's obviously not very friendly to his Tamrielic counterparts.

But as far I know, the fall of Ayleids would please Auri-El too, since they've effectively switched their allegiance to the Daedra. I think there's a new ESO book that even mentions a civil war.

He didn't abandon elves, he just stopped scorning men. Alessia is what happened to Akatosh. He changed his mind.

Of course, since he's not restrained by time, Akatosh changing his mind in the distant past doesn't mean that his previous disposition(s) aren't still working against man. The Time Dragon couldn't undo himself, but he could answer himself, correct his previous errors. Hence things like Alduin and the Last Dragonborn. It's all just ripples from an ancient revelation, one which convinced him the world was worth saving.

Minor Edits: Thank you, that clears it up a little.

kertaw48: sounds a lot like what Martin did. Too bad he turned into stone right afterwards, we have no way of knowing how much it was himself and how much of Akatosh. Though I'm more inclined to think that, at least in Tosh Raka's case, despite punny name, it is his own will, not Akatosh's

The time-dragon, with the revelation, was apparently in the business of creating dragon-borns before the whole Alessia thing.
It is of interest to note however, that Miraak did not help fight Alduin, yet at the same time was no friend of the dragons and according to some unused dialogue, he refers to Nirn as a 'chaotic world'. Maybe Miraak happened when the time dragon was still making up his mind on whether or not the world was worth protecting?

Akatosh is an insane dead god that refuses to believe he is dead, i think but i'm not sure if that's canon or just MK's theory(i forget his name, no longer works for Bethesda but they ask him for advice every now and then.)

Akatosh isn't above getting involved with affairs of mortals and usually does it discreetly. The COC was his weapon against Dagon(I think he either asked the others before consulting the scrolls to see who would be his unoffical champion or just did it without caring about the others) and the Dovahkiin was his failsafe against Alduin.

With Miraak, i think he was testing the prospect of bestowing a dragon soul on a mortal to see what worked and what didn't before he made up his mind to help Nirn. I think he was royally [&@%!] at Alduin for turning from his role as the world eater and may have intended for Miraak to kill him instead of the 4 dragonborn heros that banished the wyrm forward in time. However, it's not really clear what he intended to do with Miraak due to there being little evidence in game. I think. (I've not completed DB).

Time is the third component in the interaction between positive and negative forces. There's no dance between the two without the flow.
Time is not on any one side in the dance. It is on both sides of the dance. The dancers simply have different names for the same thing.

The concept is very old. Take an example of The Fates in Greek myth. The thread being woven can be smooth or frayed, depending upon the person's balance. But it is being drawn off the wheel at all times. Until the thread is cut.