[Will]

Ummm... I wouldn't completely lose the shields if you have organic tech. Mainly because of Crystalline tech. Also because shields provide more protection than armor. A good design should have a mix of both.

Anyway when you look at the cost, size, and damage/turn of all weapons, the EAGs are the best standard weapons in the game (meaning no special ability).

Small Lightning Rays are the supreme fighter weapon. I have a game where my large fighter design is 1 shield, 2 SLR, combat sensor&ecm, afterburners, and the remaining spaces taken up by the required components and engines. Two Groups of twenty on patrol took out a fleet of twenty enemy cruisers (I'll admit it wasn't exactly a fair fight, the ships didn't have PDC). If I had used fighters with something like Small APB, I wouldn't have been able to take out the entire fleet.

As said before, Organic Armor is very good, has the best damage/kT ratio with Crystalline, and regenerates each combat turn (try making a ship with max engines and fill the rest with organic armor. Use it to ram ships in the Sim. Watch it magically restore itself to 100% in 1 or 2 turns). You must have multiple components for this to work, however.

Then there's the facilities. A Gestation Vats/Replicant Center combo in a freshly colonized system will fill up your planets fast. Medical facility is nice, but it won't stop plage bombs IV and V. Fine for stopping random plagues though.

And finally, the already stated benefit of cost split between Minerals and Organics. This only makes for a larger fleet if you use only Monolith facilities, since the weapon cost in total resources doesn't decrease too much, only transfered between types. However, it does make for faster build times (I like using Organic & Temporal tech, Huge planets with a Temporal SY can build a BattleShip sized warship in one turn, compared to around 2-3 turns for a similar standard tech ship).