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Hopefully we will get a hot fix for this, as I can't play on any further, or we will have to wait for V13.

Haha that’s essentially my strategy when playing these kinds of games as well. As I usually want to store all equipment in one base for easy management. Keeping the features of mission restriction can integrate with the added mission types that @Ogilvy the Astronomer suggested. Maybe because you keep shooting down their ships. They instead try to change tactics to better fight your own strategy. Instead of building bases, they started doing vip assassinations using shapeshifters (vip protection), preventing tech sharing (convoy protection), throwing caesan psychics down on Earth using drop pods to mind control civilians in large cities or military bases (killing alien VIP), setting up teleportation stations to directly beam down aliens (destroy their teleportation device to stop their infinite spawning), and directly working with factions or regions that have bad relations to starve Xenonauts of funds (alien meeting assault),... In that case how well you play will directly influence the missions that you can partake in. In addition, I can suggest adding to the game a tech tree of non-lethal weapons to take out human enemies and crazy civilians (who keeps running into reapers and get themselves killed). Maybe an expansion of the shock baton/shock grenade/gas grenade research to give you things like stun guns, psychic powers for your troops, to MIB like Neuralyzers that can suppress the aliens and control the civilians,...

I'd still like it to be a feature where if you shot down UFOs fast enough they can't do certain missions. I for one needed that because I liked to have a lot of fighter bases scattered throughout the world and 1 single large base for storing soldiers. Those other bases NEEDED to be able to shoot down attacking UFOs or else they would be destroyed by base raids. Im very OK with simply making those other two missions you mentioned not require a UFO to start. As long as base assault always needs a UFO and its always somewhat obvious that a UFO is approaching, I'll be fine.