I'm going to ramble a bit about the production/economic aspects, since that seems to be what takes most of my concentration, and not in a good way. Also, I hate making comparisons to other games, but I will anyway. Blair asked specifically to post my opinion on this, since I guess you guys disagree about it a lot...
Now, a lot of this could be alleviated by some UI improvements, which I don't think we're supposed to provide feedback on yet, so I'll shove those comments to the bottom. The main source of my aggravation is having to, constantly, stop what I'm doing whenever I get enough $$$ to build a ship, find an unused shipyard, and build it. Not doing this is wasting my production capacity, and letting my opponents build ships/research tech/whatever sooner while by buildings are idling. The two obvious ways to alleviate this is the SupCom way, which might be a little overkill (and require a lot of UI work in addition to coding), and a global production queue way.
The SupCom way, for those unfamiliar, is that building something drains the resources out of you over the construction time, so if you have a $100 ship that takes 10 seconds to build, it drains $10 per second. If you run out of money, construction on everything slows to what you can afford. So if you're building 3 of these ships in 3 different shipyards, and are broke but are making $10 per second, you'll finish building all 3 in 30 seconds (or you could pause/cancel two to finish the first in 10 seconds). This is actually a lot like how most 4X handle spending, now that I think about it. Bonus points if you could intentionally slow a facility's build rate and loop build queues, so that you could say "I am going to spend $5 per second on ships at this factory, and build 3 scouts, 2 flak frigates, and a siege frigate over and over".
The global production queue, I'm not sure if I've seen before, but it's something that could be more directly thrown on top of the standard RTS resource system. Everything works normally until you try to spend resources you don't have. When you try to build something that you don't have the resources for, or if something is already in the global queue, it gets thrown into the global queue. As soon as you have enough resources to pay for the oldest thing in the queue (whether ships, research, facilities, whatever), the resources are paid and it is removed from the queue (construction starts as soon as the constructing unit becomes available). So exactly like now, except that you can queue up stuff to build once the funds are available. You should also be able to add stuff to both ends of the queue, so that you can go "I need these things now, and then go back to whatever I had queued up before." Now that I think about it, actually being able to bring up a display of this queue, maybe pop in/out horizontal bar from the sides, to manipulate it would be awesome. Like middle click to zoom-to construction location, left+click+drag to reorder, right click to remove or something. Yes... for this game, I might actually prefer that.
Minor random UI stuff. Could list lots of things if I wasn't trying specifically not to thing about it

Icons indicating whether a planet is has idle constructors or shipyards. An indicator of infrastructure level would be nice, with an additional indicator if population is at maximum while infrastructure is not. Indicators on ships with unspent ability points/unallocated squadrons without having to select them.