I don't see plot holes. I see plot loops. Alduin is Akatosh's son, yet is the End of Time, which is by necessity an aspect of Time, and since all Dragons are weaker to time shifts, as Paarthurnax says, they can't remember the divergent timeline where Alduin was just "Nord Akatosh" like humans do.
I see it the way I see Morrowind being given fertile zones after Daggerfall: improvement by addition. We didn't really know many details about Skyrim and its history outside the general outline, and while Skyrim's myriad plotlines certainly had flaws here and there I think it did a good job integrating dragons into their pre-existing lore.
And why would elves care what happens to Nords in the merethic when they're too busy trying to copy the gods?
Hrm valid point.
But the way the story is presented is very poor, and the "loops" seem to be covering for an ill devised plot more then anything deeper.
I mean, when playing through Morrowind and discovering its world and story. It all made relative sense from the get go and yet more with some investigation. Oblivion and Skyrim on the other hand. Just seems to make less and less as we go, with cop outs like non linear time being used to excuse nonsensical story telling.
Its all fun and entertaining none the less. But I'm just left with a massive "Wut?" at the end of it all. Which just wasn't the case with Morrowind.
(Not a one eye'd Morrowind fan, for the record)