1) Add turnLimit 12 and chronoTrigger 2 to strange lifeform missions. After turn 12, all remaining monsters flee. Reducing the mission frequency was a nice touch, but this would make the missions strategically interesting instead of a spamfest where only mid-long range assault rifles (or pistol equivalent if low-tech) are used.
2) Under difficulty settings, increase difficultyCoefficient or defeatScore, so that it is possible to lose in the early game on higher difficulty levels, rather than just giving up because you will suffer from having less veterans later. Maybe reduce number of enemies and increase number of monster terror missions, so that instead of being a grind, hard difficulties are actually hard to survive in. Buff score technologies so players can sacrifice their research to hold on, plus it would be nice for non-promotion-related researches to be more useful.
3) Give less (or equal?) score for arriving at a mission and aborting it than not arriving at all. From a gameplay perspective, missions where you arrive only to abort when it gets intense are not fun, and aborting is super OP. Thematically this could be seen as a failure of the project.
4) I would prefer less minor missions to shorten the game a bit. If you could implement a setting for that, that would be nice. Right now, it's a bit too easy to get a full squad of 100%-TU agents with 100% of available research covered, yet you still have to do every safehouse and such if you want to play well for EXP reasons.
5) Buff reactions/bravery melee (and slight melee in general), light armor, throwing (especially knives which seem much worse than stars), rats, dog armor, flashbangs (enemies outnumber you), civilians, lone madmen, dagon in general (so easy), bolt-actions, explosives, drone armor, reactions training, heal gel, cannons (except for explosive automatic and buckshot non-automatic), hazmat, skulljack, maybe kneel accuracy. Nerf shields, FAL and similar mid-long-range automatics, enemy dodge (makes swords much better for them than you), stims (increase cost, probably too spammable, basically just ammo for the flame glove instead of waiting for recovery for example), agent bravery (non-psi panic seems too rare).
6) Unit pages on UFOpaedia could be better. I don't really care about armor, I care about resistances, dodge, stats. Dunno why there are so many pages for civilians. But I could be wrong.
7) How about adding transformations? There are four cults, why can't I resurrect people or turn them into 10-bravery 90-psi tentacle monsters, lol. Plus I think being able to bring back a veteran soldier at a high price if you recover the corpse is pretty neat.