Your struggles are over. After many, many revisits to this mission and trying to find the ultimate strategy, I've found one that works every time, doesn't require tooooo much micro management and gets the job done!
You can also watch this video and get a full written walkthrough on my website:
scott2.neocities.org/videos/c...
All bonus objectives and intel!
The key to this strategy is to destroy the Crane, Barracks and War Factory at the South East GDI base as quickly as possible using Vertigo bombers. This clears the bottom half of the map of threats and enables us to capture the Juggernauts much more easily.
After that, we intercept the Northern GDI forces, and use the Juggernauts to disable the North East GDI base.
Meanwhile we're building a backup force at our first base, just in case GDI manages to get through to the Scrin.
Once GDI's production structures and power is down, the mission's pretty much complete and you can finish it however you want!
The Scrin last much longer with this strategy because of how quickly we deal with the South East base.
I hope this helps someone out, this mission's a real toughie.