I originally thought I could duplicate my answer from Cartoon/anime about a giant robotic fish in the sky and then dismissed it because the main character's name was Joshua and there were no space launch that I knew of... But upon further Googling,
aero troopers ending returned this review, and it clarified the missing points.
So, this is probably Aero Troopers (2003). Although it's animated, it's not anime per se as it was made in the US. Summary from the jacket:
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.
You can watch the demo for the movie below, with ships everywhere and wingsuits at 3'25:
The review mentioned above has "Micah" (actually a sidekick and not the main character)...
Joshua gains a roommate and sidekick, Micah, a sarcastic and spunky cliche who is nonetheless something of a burst of personality in this otherwise rather dull movie. Micah and Joshua share an age and a backstory, and it’s not long before they’re playing around like fools on the ship’s guns, seemingly without any sort of supervision, and naturally it is here that Nemeclous’s little aircraft minions show up to be blown away.
It has the wingsuits, as well as some pirates.
On the bright side, along with the material wings he uses to hover and fly around, Joshua gets a gun! [...] The reason? Pirates have stolen the Aero-troopers’ supplies, we are told, and the “heroes” want to steal them back.