My only main early game issues is a major tendency for many of my surface/suspicious activity missions end up taking place 'just' outside of my starting transports fuel range. Also, the difficulty of the early game sus activity missions feels very out of proportion (hello Xarquids again), the surface missions are pretty fair in difficulty and serve as a great way to gain access to Laser Rifles and X-Rifles, but the underwater missions are a weighted dice roll against the player if you even have the firepower to kill a single enemy, let alone half a dozen who all have full TUs and reaction shots on your exposed troops.
The pirate missions tend to get repetitive very fast, same map layout and literal same spawn points (there is always one cultist spawning to the direct south of the landing zone) means you'll be going through the same ship a dozen times. Does not detract from the enjoyment to a major degree but it does mean my ground tactics become very homogeneous since I know the entire layout, I suppose this is something you could extend to terror missions, but the difference is I can get multiple pirate attacks more consistently.
All in all these are mostly minor concerns, since the game has a much slower start (far more in line with X-Files than Hardmode or most other mods) and skipping or not being able to reach these early missions is not that punishing outside of loss of experience training. I do think the sus activity missions should at least for the first month or two be a bit more 'fair' in the enemies present.
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Oh, one minor feedback point. The X-Rifles lack any 'oomph' when you fire them, sounding more like Gauss rifles or a peashooter. They should use more traditional ballistic firing sounds.
Otherwise, I've quite enjoyed the other aspects of the mod so far. Good stuff!