I never felt like it was a problem that there was still evidence of the time wound after Alduin had been defeated. Timey wimey something something.
What I want to know is, where to the freaking dragons keep coming from, now that Alduin isn't bringing them back?
I've also enjoyed that there's always one (no more, no less) hold guard who notices that you've done something epic. "Hey, Dragonborn, thanks for saving the world. .... No lollygagging, btw."