TerranC,

Nice ideas. Looks like the Feds will be fun to play. The only thing I can think to add would be Dilithium Crystals. A very small component that is ultra expensive in radioactives. Somehow this should make the ships faster (move bonus? Emergency speed?)
Some comments on your many many ideas:
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Ablative Armor: Crystaline armor with slight added damage resistance but no shield energy.
Metaphasic shields: Phased shielding with slightly added strength and slight recharge rate.
I'd guess they would have vanilla shields prior to metaphasic shields in the tech tree.
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Transporters: Serves as Mine Bay, Satelite Bay and cargo bay with storage area of 50 Kt and can load cargo from ships and planets 1 sector away.
You can do
that!
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Replicators... Only effective for engines, weapons and command. Engines recieve half of the storage capability, weapons only 75% effective than original.
Is it possible to specify which components are repairable? Is it possible to repair weapons partially (only 75% effective)? Perhaps have the Replicators repair just one or two components (see organic armor I think) but use a
ton of supplies.
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Warp Core: Quantum Reactor but this generates supplies up to 80% of the original supply capabilities rather than make it limitless.
I'm guessing that 80% is for the advanced Version. Maybe the early Versions of the Warp Core would have a lower %?
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EPS Conduits: 30 Extra shiled strength. Decreased hull strength due to the volatility of the conduit.
Very cool. I like the idea of the fragile hull strength... very accurate I think to the Star Trek realm. ONce the shields are down.. yur ded!
Super vulnerability to shield bypassing weapons, which I think is just fine

I'd guess that this would be an integrated component (ie. type of hull) rather than the plug-n-play type of component.
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Holodeck: Increased Crew Experience.
I'd just suggest making this an energy expensive component to make, and that it would gobble up supplies like crazy.
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Ramscoop: Generates 50 supplies for every storm or sun. Adds 75 supplies to the generation of supplies if Warp core is installed.
Very nice. I'm not sure you can set supply generation per storm, but a great idea!
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Nacelles: Adds movement bonus. (Size should be large)
I always thought of Nacelles as just the plating that shielded the warp engines... sort of a "don't cook the crew" structure.
I love the ideas, and please just take my yammerings as constructive discussion. If you can make these techs, components and ship types happen, I guarantee I'll play the Feds.
jimbob