Thank you all for advice!
Tridus, I liked your advice of building fortresses. The problem I have is I never know how many turrets or fortresses are "enough" to stop a wave. I might be putting 100 missile turrets on the planet and think it will do just fine - when the next wave of AI comes in and wipes them all out!
Is single fortress sufficient vs. 1k wave of ships?
Honestly I think it's something you learn with practice. You want to have some backup ships in case stuff breaks through, but you can build a defense against huge waves and Fotresses are a part of that defense.
The thing is that one Fortress can handle 1k fighters with ease, but will get destroyed by 50 bombers if it's alone. No one defense can hold off everything the AI has. So you need a more layered defense on a planet, as one of the links demonstrated in this thread.
The nice thing abot Fortresses is that they have very large range (hold down Z while pointing at one and you can see its range), and they can move (very slowly) to be positioned optimally. You want to put them behind other defenses and let their range protect them from things like bombers, while they flatten other types of ships. They also have the ability to repair (as do mini forts). Tractor beam turrets near the wormhole will hold ships in place and let your turrets hammer away at them. Put a forcefield over the tractors and they'll hold longer. (Hardened Forcefields are a great unlock, not expensive to get extra FFs and some units can barely scratch them.)
On a planet I really want to hold (like one I'm setting up at a choke point that I know will be attacked) I'll put tractors at the wormhole, two mini forts near the wormhole (to repair the turrets), a big fortress farther back. Build at least one remains rebuilder, which will rebuild destroyed turrets and mines automatically (your fortresses and any engineers can repair them).
Then I'll put down some standard turrets: basic (needler), laser, missle, MLRS. Snipers well back, or Spiders if I have them. A Heavy Beam Cannon for sure. If I put a forcefield up near the wormhole, flak or lightning underneath it (those are okay under a FF, most other turrets aren't). Put mines around the wormhole, or between the wormhole and what the AI is likely to attack. Normal mines early on, EMP or Area Mines if you have them. Then I'll use a millitary command station for the attack boost on the turrets and the cloaking detection. (I tend to get mk II Millitary Command Station once I have an important building to unlock, and if the game goes long enough mk III for really key things like the advanced factory.)
If you have multiple wormholes attacks can come from then it's a bit different and I may cluster the defenses more around an object instead (like the advanced factory), but I'll use the same set of buildings. I don't typically use gravitational turrets, but I should.
I'm still learning the game, so there's things I need to incorporate.
For defensive helpes, Leech Starships are quite nice. They can reclaim a lot of the stuff in waves and make them your ships instead, which really boosts your defensive firepower. That's why I use logistics command stations behind the front line: they let me move my ships around between planets VERY quickly. Just mk I, I typically don't unlock higher ranks of that, but you might find them worth it (higher ranks slow down enemy ships by larger amounts).
Note that unlocking millitary stations also gives your home system the attack boost from the station, and the cloaking detection. mk I has a narrow range of cloaking detection, mk II is wider, and mk III covers the entire planet.
Also, I did unlock harvesters. I unlocked basically everything - because I've been focusing on researching only econ stuff, while my friend researched ships only. So we effectively x2 our knowledge, kind of.
Neat! Personally I wouldn't unlock both harvesters and economic command stations, as they serve the same purpose.