Well, if it helps, people seem to accept that Lorkhan = Shor =Shezarr, but getting past the idea that Auriel = Alduin = Akatosh can be difficult, due to the [censored] imperial's dilulted and widespread belief, due to politicking and Akatosh being portrayed as a good guy in nearly every game.
Even Tiber got the idea, but knew how to handle it better, by being Talos, instead of instituting Shezarr again. Talos is pretty much a stand-in for Shezarr/Shor/Lorkhan. A much more acceptable deity for everyone, save for the Altmer of Summerset Ilse, who are more hardcoe than the nords are with Shor and their anti-merrish belief.
It's not so much the idea of widespread dilution so much as the fact that Alessia and Marukh made Akatosh so different from his original. Linking Shor to Lorkhan is easy because they are consistent, pro-human, anti-elven, brings the Aedra into creating the world. Akatosh was changed to be less anti-human and to symbolize eternity rather than transience. Once all the pacts were broken, the Akatosh-aspect is like to just disappear into nothing. Not only that, but people got unfortunatelyentrenched in thinking of him as a "good guy," so they react with surprise when they find out they were incorrect.
Are we even sure we are fighting Alduin?
Last i heard that was all speculation just because we are fighting dragons and he is the dragon god of time.
For all we know we could be fighting the Ka'Po'Tun and there leader Tosh Raka (whom is the worlds largest Dragon at the moment)
The devs have said Alduin, since the very first bits of real information in the gameInformer reveal.
Alduin is certainly not Akatosh. Alduin is the time-eater and Akatosh is the king of the Divines. If Akatosh was Alduin then the Dragonborn would have been killed the second he/she was born. Since the Dragonborn is alive and is destined by the gods to perform an important task then that means that Akatosh wouldn't want the Dragonborn killed.
You're looking at it too simplistically. Read the linked Aldudugga. Alduin can't eat the world until Dagon chips it down small enough for him to eat. Also, Time is Time, Alduin and Akatosh are just too ways of literalizing the metaphor of transience and eternity. Also remember that no Aedra is absolute on Nirn. That was always the plan. Shor made several of them take part in creation so that, unlike Daedric Realms that are wholly extentions of a single will, Nirn is a place where people can make decisions and there can ever bee surprises.
But the biggest issue is the idea of Akatosh being good. He was always a destroyer-god as Auriel, but the elves considered the end of the world to be good. So in the Nine Divines, Akatosh retains the position of "good god head of the pantheon" but given the eternity symbol to make the Empire seem to be an eternal and legitimate power.
Think discworld, only dead serious and with some things at the very beginning that are always the same no matter what the belief is.