Exactly!
Your solution is too simple... if I give player a way to consistently prevent infiltration, he will just prevent infiltration every time. I might just as well remove it from the game completely.
You do not understand the idea. And it is that at the beginning of the game the player simply has nothing to fight with large ships. There are no ships capable of catching up with the enemy, no weapons to destroy it. And with the development of technology, it becomes possible to prevent the most aggressive alien missions. That's why new ships are needed. Otherwise, what is the point in the speed of interception, if in general, to prevent a mission impossible?
Otherwise, there is no point in developing them. You can play with one base and fly on interceptors with plasma cannons until the end of the game, since Is wasted in the of Lightning and Fire Storms inexpedient, and with the invention of the Avenger, build it in a single copy and immediately fly to Cydonia.
P.S. And in general - this is nonsense. Their ship was shot down, but they came on foot and built a base or organized infiltration. Why the hell are they ships if they walk at such a speed?