Some of my own:
Ability to include more than one of ship/shipyard/starbase as a target
Similar to horemvore's suggestion with improvements, put (ship) or (starbase) in tooltips so players know what is effected, as well as tags like (fleet) or (enemy fleet).
Ability to create new artifacts and resources to be placed on the map.
Let us create abilities that do more than throw stats around, like Ancient. Even if a boolean toogle is the only thing, we can do a lot with that.
Let us append into existing entries(components/improvements/etc) for better compatibility.
Make <target> able to target individual items(components/improvements/etc) more specifically than it does. Manufacturing can be added to colonies, but I want to add more manufacting to improvements, more damage to lasers, etc.
The game not crashing when a tech has more than 8(or was it 7?) icons on it.