Sounds like Netstorm: Islands at War.
Played 15 to 18 years ago - it was released in 1997, so entirely possible
Took place in the sky - check
Collect crystals - check
Construct bases - well towers
Had mules - the workers were horse/mule type characters
Enemies on seperate islands - check
Scorpion like enemy - I could see how some of the enemies could resemble a robot scorpion.
Build bridges - check
That would fall down - they could be taken over, I can't remember if they could be destroyed.
Top down view - see below
