See I don't like to use missiles. As you said they are usually shot down. It is just so much easier to go right up to the enemy's front door and bomb then by strike fighter, bomber, or even just cruisers would do the job. But, if I would have to use missiles or some type of projectile, they would have to be launched via kinetic bombardment. In reality, you can not shoot those down because they travel to fast. Around mach 10 or an estimated 7,700 mph. But since kinetic bombardment is so powerful, I would suggest that a player is only allowed to make 1 of these and that there is some type of anti-satellite weapon. Both would also should be unlocked late in the game. And there should be a limit to how many are up in space at once. But overall this would require a massive update to just add these couple of things to the game. But adding this could also bring in new players and could lead to an even brighter future for CON. So honestly, just try to take over whatever part of enemy lands you are trying to take over, but if you can't you should always try missiles.