Aero Troopers (2003)?
From the jacket below, which features a robotic-looking fish (and what do you know, it's got Mark Hamill in it!):
In a world beyond imagination where fantastic tree villages float in mid air, a young boy named Joshua dreams of adventure. Forced from his home by an evil mechanical beast called Nemeclous, he discovers a fantastic world high above the clouds. There he must join an elite force - the Aero-troopers - who are sworn to protect the skies. Joshua now finds himself on the kind of adventure he has always dreamed about... but little does he know the entire fate of the skies lies in his hands.
The follwing demo video contains various clips from the movie, including some wingsuits at 3'25. A comment by the poster (who apparently worked on the movie) explains it was made with the 3ds Max animation software.
Found with the Google query
anime "floating islands" "robotic fish" which returned this Reddit thread on which someone (you?) commented:
I have been searching for this same anime. they end up fighting a big robotic fish that eats the floating islands. I cannt find it anywhere, and I thought the title was "aero soldiers".
Aero Soldiers + Sky Soldiers + a Thesaurus lead me to Googling "aero troopers" on an off chance, and jackpot.