I had the same issue. after several turns (especially in the late game) the performance becomes atrocious! 

Use ELCP (Endless Legend Community Patch). Those are likely from errors in pathing from the AI.

ELCP is the best solution to those issues and it has a ton of benefits besides that. I can't recommend it enough.

I had the same problem. Putting Endless Legend.exe in the exception list of my Antivirus program solved it for me. No more lagging.

(As being indicated in the read first-technical troubleshooting section in the forum).

I'm also experiencing a lot of stuttering. I can play Humankind fine, but not Endless Legend. And I don't think it's the AI. At the beginning of a game if I click and move the map around, it stutters. Also, the opening cinematics stutter as well.

I've tried playing with the lowest settings and I've uninstalled all the DLC but nothing works.

My specs are:

Desktop PC - Windows 10 - 64 bit
AMD Ryzen 5 3600 3.59 GHz
32 GB RAM
Radeon RX 580 8 GB

Just discovered it's because I'm using two monitors. For some reason this is causing the stuttering. Hope someone else finds this helpful.