First of all, sorry for necroing this thread years after, but since we don't (and we won't) have any official response or fix from Ubisoft, here is my explanation and recommendation.
The game uses Unity (probably some build that is pretty old by today's standards) and Unity has very poor performance unless you optimize it very well (for example, its renderer uses only one thread which is probably one of the things that is going on in case of MMXL). So combine that with time constraints, rushed release, and team with no previous experience with this type of game, and you have a recipe for disaster right there. Limbic was probably very well aware of all this because they moved to Unreal Engine with Heroes VII... and H7 runs like a charm on modern systems. MMXL does not.
I am re-playing the game right now, gameplay-wise it's excellent, but you just have to accept its poor performance. The performance issue has been with us ever since 2014 and Ubi dumped support for the game long time ago, since it doesn't milk them money, so I'm afraid we're out of luck unless a miracle happens. Believe me, I tried it all...
MMXL uses about 15% of my GTX1080 in forests around Seahaven, running well below 30 fps. CPU usage sits at 100% load on two cores all the time (i7-8700K), so the engine implementation is brutally CPU bottlenecked. It appears that it uses one thread for rendering and the second thread for everything else. Also, the big sutters many experienced are due to the game loading assets. That's also why you see some things like trees and rocks suddenly pop in to existence as you stutter around - the big stutters and fps drops are caused by the game grabbing data from your drive, so SSD helps a bit (at least the stutter is shorter on an SSD). It also never goes above 2 GB RAM usage and always stutters at exactly same tiles. It's just a terrible implementation, really - single-threaded game with pre-defined loading areas instead of implementing asset streaming in the background or just dumping all the data into RAM, provided your PC can handle it.
There is no way to run this game faster given that we don't have access to the source code. At least until single-thread CPU performance drastically increases - by about a factor of 2 or 3 - we are out of luck.
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