I didn't play SE4 much but did enjoy SE3 quite a bit so sorry if some of these are already in.
-Nomadic race style. This race would for some reason or another have abandoned their world. Instead they live in space stations or orbital stations. (at the very least, stations with populations would be nice). Maybe even a special tech to allow mobile habitats.
-More personality to Organic races. Maybe growing everything rather then building it. This way they'd use nearly entirely organic resources. Maybe with a longer build time to compensate.
-Similar change for Crystal races but with metal used entirely rather then organics.
-Larger ship classes. After all we get to build planets
-And of course better AI.
