I really think the aliens should be smarter about what and when different missions are selected instead of random chance. It makes sense that early on the missions would be primarily scouting missions and then moving onto alien base building and subjugating the human population missions (bombing, terror, military attacks.) The more that UFO missions get shot down before completion the longer it should take to move onto the next stage. But shooting down UFO's and hindering the alien invasion progression should then provoke an angry response from the aliens. They should begin to look for and attack Xenonauts bases more and more frequently with more and more UFOs in waves getting dedicated to Xenonaut base attack missions until you get entire UFO waves attacking Xeno bases from multiple directions, eventually assaulting multiple bases simultaneously too. They should get pissed off and start dropping orbital drop pods into Xeno bases with like 20 reapers on board. They should start better defending themselves with more and more fighter escorts for their troops transports. The aliens should become better and better at defending themselves, they should even try to send defend and rescue missions to their fellow alien buddies at crash sites and attempt to shoot down troop transports enroute to crash sites. It is fairly dumb of the aliens to allow un-escorted troop transports to travel for 18 - 24 hours each way to and from UFO crash sites and kill their buddies and steal valuable technology.
The UFOs should also be making a beeline for your bases. They know where you live. Yes it might be easy to stop when it is just one UFO incoming. But later when they realize that sending one at a time isn't working they should be sending like 4 UFOs to a base. Also makes sense that they would begin their approach close to the base or sometimes even directly on top preventing even the opportunity to intercept the base attack transports and forcing you to rely on the defensive batteries and your base troops.
