I would suggest that with the Dark Avatar expansion that Stardock would improve the scenario making process by allowing more things to be set.
I found it really odd in the campaign scenario 'Salvation' that Earth was not set as the Terran Alliance capitol, had only one billion people, and its only improvement was a starport. If you were able to set things like civilization capitol world, improvements, and population, you could give scenarios a lot more flavour.
With each scenario in the campaign, the lack of any improvements on the worlds you start with make you feel like you're starting from scratch. The only decent explanation I can think of is that the scenario's starting worlds were 'just colonized', but that obviously wouldn't work with Salvation.
One more thing that I would want to be able to control in a scenario is being able to place starbases at the beginning of a scenario and being able to choose modules for it to start out with.
Does anyone else have suggestions for what additional improvements can be made to scenario making?