Given Zodiark was reshaping/redirecting the world's aether currents to ward off the Final Days, some manner of negative feedback from everything suddenly snapping back to how it was before seems expected.
The FSH quests bring up how fish all over the world were suffering from bouts of aether sickness due to the aether being shifted back from the heavens to the earth below, which was an immediate symptom, but perhaps something deeper about the world's workings has been disturbed.
I also noticed that the number of "wedges" that need to be driven into the figurative serpent's back also happens to match the number of shards that are remaining...which is stirring up even more thoughts about the potential implications.
safety spoils for EW ending
What if the world was only able to sustain itself to Zodiark and Hydaelyn's presence and now it's due to slowly unravel unless the shards are somehow "linked" to the source to stabilize the flow without destroying them?