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 separate 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:

[![Top-down view of the edge of a map, depicting a floating island with several constructions][1]][1]
[![Netstorm poster, night sky with a lightning bolt][2]][2]

[2]: https://i.sstatic.net/KAmIK.jpg
[1]: https://i.sstatic.net/B9jQB.jpg