First of all, it looks good! I'm definitely interested in seeing the finished product. Now for the specific comments.
RE: Small ship sizes being useless--If you use
massive swarms of small ships, you can easily destroy even dreadnaughts. I've used DS with ECM 3 and stealth armor 3--total of +95% defense modifier--in fleets of 20~30 with success. Of course, you will lose ships each battle, and will need to be replaced quickly. Supply may be a problem, too.
RE: Damage to supplies--Would be a neat idea, and I think it's been bounced around before, but I don't think it's possible w/o a hardcode change.
RE: Organic unit damage/shield regen--Game currently doesn't track partial unit damage, so it doesn't regen partial damage either. Auto-regen ship hulls sound cool, though.
RE: New racial traits--I think Megascalar/Microscalar sound great; maybe a nice combo! I love packing out ships with as many gizmos and gadgets as possible, especially extra big ships.
RE: More constructed-world sizes--Mostly eye-candy/fluff, but nice eye-candy and fluff. I also love building worlds.
RE: Space Yard hulls--I think this would be great--especially if adding a SY component causes the build rates to stack like it does with facilities.
Overall, can't wait to see it!