There's clearly issues with balancing resources, but all the resources aren't even in the game yet.
I think, in general, the bonuses from mining need to be more substantial and/or have a wider area of effect. A single ship getting a slight buff (though the buffs I've seen don't seem particularly great) is ridiculous.
On the other hand, I think that there's an interesting mechanic here with resources having discrete benefits. If a faction is falling behind militarily but they could take their mined resources and generate a single "experimental" ship that was far more powerful than anything else in their fleet, that would be cool.
I'm not really sure what the tactical battles are going to end up looking like (come on Stardock! can't you give us a hint?!) but if we end up with direct control, I can see having those "experimental" ships being a champion type unit, with special attacks and the like.
But then we get into what the hell are they going to do with tactical in this game. If you have thousands of planets, that means in the end-game there are going to be way too many ships.