I know that beta 1 was supposed to be about compatibility testing and not gameplay, but there haven't been too many bugs to find, so I'll write up some thoughts I had on my favorite units, the fighter/bomber squads.
I'd like to see small craft have an endurance timer. By that, I mean the amount of time they can spend undocked from their base should be finite (instead of the current infinite). You could have a research tree to increase the timer to give small craft more range / attack time. I think this would pull the hanger platforms closer to the battle and give a risk/reward tradeoff (right now, it doesn't make sense to base the hangers anywhere dangerous. Hanger location only helps the initial travel to the combat area right now).
I'd also like bombers to perform one (more powerful) attack on ships and then have to return to base to reload. It doesn't make sense right now that the bombers will continually attack a target one-missile-at-a-time rather than just firing all those missles all at once. I think an attack of, say, 4 bomber squads should halve a capital ships's shields (or worse).
More (potential) research topics for small craft would be to increase hanger capacity (allow more squards on the carrier and hanger platform). Increasing carrier experience would result in faster turnaround time for the bomber rearm or small craft refuel rather than the current "more squads" bonus. I think max squad limits of 4 for the carrier and 4 or 6 for the hanger platform would be about right. The hanger platform might need to be upgraded to get the higher squad counts.
My final thought would be to remove the separate fighter/bomber squads and have just one type of small craft. There would still be fighter (i.e. anti-small craft) and bomber (anti-ship) roles, but the squad could switch roles with a dock+rearm rather than the current remove (fighter|bomber) and add (bomber|fighter) management we have to do. Squads would auto-build as a slot opened up, and the squad management screen would let us determine fighter/bomber role and launch. In space, we'd have a dock and a dock+change role button in the special abilities pane.