First of all i have to point out that for a beta this is a most impressive game and i'm pleased to see new ideas being implemented (which makes you a rare breed of developer, as many give the impression of not listening at all). However since this is a beta, and you need feedback i thought i may be able to provide some.
Firstly, ship combat. It's just not quite 'right'. As a Battlestar Galactica fan i very much like the multiple targeting and the usage of kinetic based weapons (because you know, it generally looks awesome) however right now there's just something very 'flat' about the combat. To me ships should be making strafing runs and not just being stationary as all but the fighters seem to be. It's a minor complaint in reality, but to me it would just add that extra bit more.
In terms of how ships looks, mostly very impressive. Definately very impressed with the Carrier Capital ship; it has those very human qualities that reminds me of the first Human designed stargate ships (the prometheus i think it was called). However both the light and heavy cruiser feel wrong. With regards to the light, looking at it from the top i think, 'yep, nice and fits with the back story'. However the side view makes it feel a bit too high tech in look (and then weak when it fires its pee shooters). So for me that model needs some work. As for the heavy crusier, well it looks deliberately ungainly. Whilst yes, it does have that trader feel, it feels like a ship that shouldn't have been converted to combat. Again, as with the light cruiser, something just isn't right for me.
The ship design is actually opitimised in the Flak frigate. It looks nice and simple, which is the perfect look. Someone has simply stuck flak guns on it and it's taken that role.
With regards to the Kol, well you've already said that it hasn't had the same level of refinement, so i'll merely state that i'm another person that doesn't particuarly like how it looks (although i think every warship should look like the Battlestar Pegasus, but oh well).
An idea i would absolutely love to see implemented is the admiralty idea from Conquest Frontier Wars. The admiral would allow you to group ships into fleets (rather than the ctrl method, which never feels very 'fleety' to me). Plus each admiral would have a prefereed ship, and if aboard that ship give it a bonus to it's performance as well the fleet (such as increased range).
As for the research and economy side of the game, no real complaints from me. Maybe a bit more diverse research tree, but otherwise seems to be working very well.