How can you protect the solar system and not just

[Nappa]

planets or warp points?

[Starhawk]

System gravitational shielding protects enemies from opening warp points or nuking planet's/stars with thresher torpedoes or nova bombs.
Unfortunately for you this means you also can't open warp points or nova bomb that system even if you see a 2,000 ship enemy fleet taking a stroll through it.

Now if your talking conventional tactics well you just lay a crapload of mines in orbit of your worlds, or take my personal favorite create a new class of battlestation that is both shipyard/fortress and place a few of them in orbit of a planet, add to that a surface battery of two or three heavy weapon platforms and you'll do pretty well against most small fleets.

There's virtually nothing you can do to stop a dedicated major assault fleet except meet it with a superior fleet however.
UNLESS of course you are fortunate enough to have a star on a warp point that happens to lead to enemy space, in which case you create a "fortress world" as me and my best friend call them.

In other worlds a Sphereworld with a few dozen orbital forts, a small defense fleet and anywhere from 100 to 200 weapons platforms mixed with a generous amount of shield generators.

I personally have taken down 300 ship enemy fleets with such defenses and if the AI ever masses more then 400 ships your already in a lot of trouble but you can still cause such havoc that even the AI will think twice about continuing the invasion. And it would definately stop most human players in their tracks for anything sort of a total allied assault.

[Alneyan]

Scrap the bloody facility if you *must* take down that fleet, and it is in one of your systems.

If you really want to live in peace, you could only leave one wormhole leading to other systems, and build a *nasty* fleet right on that wormhole (everything you can think of, and then some more). No more wormholes can be created once there are 10 in a system, and that facility also prevents wormhole opening.