I have a few comments:
1. Ion mark 2 are excellent throughout the game provided you can get good ones. Celestial ones are particularly good. If you can get em with 800+ range, putting the 900-1000 range ones on your allied ships this helps a lot. Make sure you pick up Autofire as they can triple-shot and still maintain adequate accuracy with 1 upgrade. Then buff their hull/shield dmg. They fire so many projectiles that they swat missiles/rockets/fighters easily. They also "stick" enemies in place once they hit thru shields.
2. I dont get F at all. To rescue the battlestation you know you can CHOOSE where you warp into right? It took me a bit to figure this out. You simply jump right on top of the battlestation, sit right in front of it so it repairs you while you tank the damage.
3. Megaplasmas are solid, not terrible. They are designed for long range combat.. only take one with 1200 range and do NOT upgrade its recycle time. One hit will drop enemy shields entirely. They do decent hull damage too.
4. Mixing rockets isnt always a great idea. Rockets/Missiles penetrate shields which means comboing them with other stuff is inefficient. You are dropping enemy shields and wasting their shield-penetration. The only time this is a good idea is when you rely a lot on fighters as the missiles/rockets will help tie up their point defense while your fighters blast away.
5. Nukes are pretty decent IF comboed with rockets/missiles and fighters as above to tie up point defense. Otherwise they are useless.
6. Shield boosters come in 2 varieties. The point defense vesions are awesome. With 12 slots, you generally want 8 of those slots or even 10 to have them. Only the front 2 PD slots or maybe front 4 should have actual PD guns. Depending on your opposition's number of missiles.
The Red big slot ones should NEVER be used, as the loss of firepower is worse than a bit of extra shield.
Shield RECHARGERS on the other hand are kind of useful, especially if you find one early game....it can save a lot of repair cash.