Slitherine

The Messari don't really fill the role of 'huge alien threat' they're supposed to. Aren't they meant to be this big force that is so dangerous all other activitives, wars etc must be suspended? As is, even the AI barely breaks as sweat as it walks all over them.

I say upgrade the Messari. With the AI now being as dangerous as it is the only players who will ever reach the Messari invasion phase will be those with a solid grasp of the game. The Messari shouldn't be a secondary threat when they arrive, they should be THE threat.

Is this with "Very High" Alien-Aggression?
While the AI is better, also note that the tech-pace has been significantly altered. With the old tech-pace you could be in Transcendance-Era when the Messari arrived.
With the current one it's more like early-to-mid Mechanization-era. And fighting Mechs with 60 strength when your strongest units are roughly at 30 strength means you will have some unavoidable losses.

In one game I had been "blessed" with 4 portals in or near my territory. And I definately was forced to concentrate my powers on those and when I was done, I was no longer in a position to pursue the Noxium-Corp as had been my plan before the Invasion.