I've run into - often - small inconsistancies with the attachment points on ships. Often, one side seems perfect, and on the other side of the ship, a couple points are buried just beneath the hull - still visible - but it throws the whole design slightly off-kilter. Last night I ran into a ship with one backwards hardpoint, where it was facing forward on the other side.
I know it's purely asthetic, but I've actually scrapped designs and refused to use certain hulls because they just don't look right to me when I'm building on them. Often, I also find myself wishing for just one more hardpoint somewhere in the middle ... again, asthetic, but something I wanted... and on larger hulls, I'd certainly love to see more points for attachments. Smaller hulls I can understand as less versatile, but Large class ships seem to have as many points on them as Small ships, but are triple the size.
Sadly, I can't recall exactly which ones put me off the most, but I could try and find them if you wanted, and attempt to describe in detail what's off. I'm sure some sort of 'smoothing' is in the works before the final version, I just wanted to give an opinion.
Also I still have two extra components without icons in the selection window - the 5th and 6th from the bottom.
On the whole, though, I love the system for designing ships, and I love the new components you included in the latest Beta ... This game just keeps looking better the more I play it and get used to it!