Metzelmax: I dunno if in the end i will include more ships of any faction, but the ftl jammer is reserved to another faction. I cant give the ftl jammer to another starfleet ship, since other factions will need it (just to give em something...).
About the Rock plating, i cant do anything about it.. sadly. If i want the Borg to feel like the Borg.. that plating value must be there, and since there is no way to make custom augments..

just take the Rock ships like more challenging ones, and thats it.
DryEagle: Yes, u read my mind. I was thinking on the arsenal of the Jem Haddar, and as u said, all the weapons will have shield piercing, but not too much (well, i need to make 1 weapon with great sp, if not it will be a bit pointless). About the crystal shard, the problem is to make a custom retalation proyectile. If i change it, the in-game crystal ships will have the same... i didnt check it, but i think there is no way to make custom proyectiles as if they were new weapons for that augment.. im a wrong?
About the Borg shields. Even if they claim to use shields, u will never see a shield on a Borg ship, as far as i remember (with the exception of voyager, in some episodes i think). The borg shields are not the same as an usual ship shield, it is a plating shield, like a reflecting field or something. But, there is a reason u will never "see" a shield in a borg ship. Even if in some episodes they talk about em, Borg ships are designed for operate without shields. The structure of a Borg ships is filled with layers and layers of strong hull plating, precisely to compensate the lack of shields. This is the design that was originally made but evolved in "why the hell, we need to give borg shields, so we can talk about it in some episodes". In Trek Core they said that this was really a funny thing, because they were laughing if the Borg could have the same shield structure of any other usual ship. Imagine if its hard enough to hurt a Borg ship, if they have shields like the enterprise... in a lot of scenes u will see any ship attacking a borg cube with proyectiles but the borg shield is not showing up any shield. But then u look at the impact of the phaser array, and u can see how the energy is reflected or kinda , probably because of that Borg plating i talked about.
This is a tricky thing.. lol. But as i said, the Borg should have A LOT of augments, but its impossible.