In my opinion, there only two real ways to defend a chokepoint, that is with a good warning system, hangar bays and jump inhibitors. (Big Fleets dont hurt of course)

The best thing to do when faced with the challenge of holding onto that precious stronghold is to capture at least one planent in front of it. All empires have a tech that allows you to know when enemy forces are approaching. If you can get the tech that allows you to see hostile forces up to two jumps away. With this you would be able to see enemy invasions up to three jumps away from your chokepoint. This would hopefully give your fleet time to arrive, or at least get their faster.
If this plan fails then your best bet is to have hangar bays. Many people argue the usefullness of these but if you can build at least four, that gives you eight bombers. And if you are playing with the advent you get THREE PER HANGAR!!! This increases your fighters to 12. That is a pretty nice force. Coupled with my strategy for using early warning they will be able to hold off an attack in time for your fleet to arrive.
And when your fleet arrives hopefully you have enough firepower to either eliminate the invaders or make them flee. If they retreat your handy dandy jump inhibitors will be there to slow them down enough to hopefully destroy them completly.
There you go. That is my way of defending a chokepoint.