The whole point of the starbase is that it is powerful. A fleet of Illuminators probably won't be able to take the same amount of damage as a fully upgraded Starbase, with repair bays, CSPs, mines, and gauss defense platforms. In fact, if your smart and use the starbase as the main hitter and build loads of fighters and bombers, then the Illuminators won't take out the base, and of course, your forgetting that a 5 kilometer battle station can absorb hits that would destroy heavy cruisers without even feeling it. It can be armored as heavily as the defender needs, and your forgetting the shields a ship that large will mount.
All very good points to remember. The main focus behind the Starbases is to allow a player to set up a focused defensive position (hopefully in a nice chokepoint), where all of their planets and other goodies are protected and then said player can concentrate on just using his fleet to launch his own offensive. Hence, the need to have these cost so much. A player should not be able to have more than 1 or 2 at a time...then the game would become too skewed.
The interesting thing is...who will be able to get one built in a well that you enemy owns, where you are planning to attack. If you can get a builder in the well and keep it protected long enough to build the Starbase and then launch your offensive against that planet...hhhmmmm...then you can use the same Starbase as a defensive unit once you own the planet. Getting some very interesting thoughts going on over here.