..dragons returning to planet nirn, then why are they still there after he's defeated? You'd think the storyline would mean that when the big boss is dead, his dragons (his serpent servants) would disappear too. Obviously from a gameplay POV they need to be there so that players can have fun killing infinite dragons. But does the need for the game to still have dragons after the main quest is done make the story flawed? Or was the world only going to end by Alduin single handedly destroying it, and the other dragons weren't important for that purpose anyway?

He raised them from the dead, and they're still alive after he's dead. Though, there certainly doesn't seem to be a shortage of them....

Yeah, and the fact that the Word Wall dragons respawn without souls seems contradictory to the storyline, but while a certain percentage of people will complain that it doesn't make sense that dragons keep spawning after Alduin is 'dispatched' another percentage would complain that they can't get anymore souls for the words they may not have gotten before finishing the MQ. I just chalk it up to Bethesda trying to keep people from complaining that they can't get the "rest of the words" if they finish the MQ before finding all the Word Walls.

I am good with the Dragons still being around after Alduin. I am not good with killing what is obviously the same dragon multiple times.

It's not the same dragon. It's extra # 1283.