It's a bit strange that we have movement limited to phase lanes, creating chokepoints - and then can't use these chokepoints properly to blockade enemy movement.
Right - you CANNOT set up or use choke points, so don't even try. It's simply not the game dynamic they were trying to create, strangely enough.
You have been given advice on using fighters, however on a recent thread I discussed my experience in trying to use fighters, including going advent (with carrier), obtaining and upgrading hangers, etc. They won't stop the siege frigates from getting to your planets, nuking them, and then leaving, so don't go that route.
Someone else here suggested planetary defenses, however that's incorrect too. Planetary defenses are just weak - that's obvious. A developer stated on this forum that this was by design - he said moderate defenses were just enough to stopping a few thin pirate raids, but that's it.
I think the game dynamic they've forced you into is to be mega-offensive with your ships. Just be super-mobile - think of yourself as a migrating type of society that is always on the move. Don't build defenses - carry colony ships with you to plop down new colonies as they take out your old ones. Build your own siege frigates to bomb him as he bombs you, etc. Doesn't suit me, personally, but if you want to stick with the game, you can try it and see if you like it.