From the general comments, it looks like most people like the idea of stargates and their varying sizes for moving around, but not for deployment purposes.
I originally said I didn't like reserves/deployment, but thought it'd be a good compromise to support empire-wide production and trading ships. So here's a chance to try and work out a system that don't require reserves/deployment.
Since the game now handles ships on a per-ship basis, trading ships can be just a matter of selecting ships from your fleets and simply handing it over. When you give an empire your ships, they just change owner, but stay in the same location. So they will have to move it to their empire, but they could use your stargates if you have travel agreement. This part won't be a problem, and will allow me to remove reserves/deployment.
Now for the hard part: Construction of ships using empire-wide production. I'm sticking to empire-wide production, so per-planet production is not an option. One reason is the space-based races that don't even have planets to produce ships from. So we will need a system where we can decide which system to produce ships at.
I could add an option for which system a ship should be built at in the production screen. However, there are several problems that I need to solve:
What happens if the ship is halfway built, and you lose control of that system to an enemy? Is the progress lost? This would make sense because if a factory is destroyed by a bomber, the progress there are lost.
Should systems that have planets owned by you, but are being orbited by enemy fleets not output any production, research, or commerce because they're blockaded? This again, makes sense, and can really cripple you if the planets there are rich in resources. If it's your last system, then you're doomed.
Should the list of systems available for a ship to be built at be determined by the fact that you have a fleet or own a planet in those systems? Fleets are mandatory because of space-based races.
If you guys agree to the above approaches to the problems, then I will remove the "reserves/deployment" totally, and have stargates be just a tool for moving around the galaxy.