This would work even better then in WarCraft III, where it was pretty tedious.
Sandbox GC isn't inherently bad. It presents quite a few advantages, however, the way it was created in E@W made the mode really shallow. 1-on-1 GC isn't very interesting. Hopefully, with a 3rd faction and some less emphasis on it being a "sandbox" mode will make it better.
I still think that 1-on-1 with dozens of neutral planets that you need to either conquer through force or persuade to join your cause would have been the best, but you know, dreams are dreams...