Endless Space has a complex, but usable UI. There is a lot of information, but for the most part it makes sens and is presented where you expect it to be. Unfortunately, I found ship building to be hidden away more than I expected. Once I found it though it made some sense.
Building ships in Endless Space uses a queue like most RTS games. Once you click on a system that you hold you choose the Ship interface at the lower left and then you click ship designs that are available to queue them up in the middle.
The ship designs can be modified and after the ships are created you can view the ship hangar to create the fleets that fly around.