Defending against invasion is incredibly tiresome. (Especially if you are foolishly attempting to complete the "Against the Tide" challenge. )

Here's why:

1) Starbases represent a significant investment of resources and production, but they become really weak in the mid game. Even upgrading them with defenses, they are easy to knock out and need to be defended.

2) Shipyards are also very weak starting mid game. If you don't defend them, your enemies will take them out first, which slows your production down because you can't build ships until you rebuild them. That's effective like losing a ship in battle.

3) You suffer a -10% approval penalty if you don't have at least one ship in orbit over your planet, but there's no real strategic reason why you would want to do this instead of defending your shipyard or starbases.

4) Your colony planets are easy to pick off, but your Core Worlds rely on these planets for manufacturing input. Losing those inputs means you produce fewer ships. However, if you send ships out to defend/reclaim those planets, you leave your core worlds/ starbases vulnerable. 

Having to split your fleet leaves it vulnerable to big invading fleets, but keeping all your ships together leaves your resources vulnerable. It's lose-lose either way. 

If I were designing this game, this is what I think I would do.

1) Remove the silly -10% approval penalty or make it so that you only have to have ships within a specific range (not orbiting the planet).

2) Add new technologies or edit existing technologies to provide bonuses like "+10% hit points to starbases and shipyards" just like the bonuses to missile/beam/kinetic weapons. This way they can scale better throughout the game.

2a) Or possibly give a small hit point bonus for each module a starbase has installed, so that the more developed your starbase becomes, the tougher it becomes as well.

3) Allow us to rebuild command ships that get destroyed. (They should require a new commander.) Losing one of these ships inflicts permanent damage and can have a huge impact on your future fleet strength. This incentivizes the player to keep the fleets big. Being able to take risks with command ships would open up our strategic options.

4) Make it so that military bases keep non-military bases and shipyards safe, similar to the way they used to make planets immune to invasion. I believe this is necessary to give the player adequate time to respond. An invasion happens over the course of several months, but you can lose a starbase in just one turn and it can take much longer than that to rebuild it to its former strength.

Ok, that's all.