1) More customization for developing your planet.
I feel planetary development is too bland. I think each development upgrade can be spiced up a bit.
For example with Develop Infrastructure you can upgrade a planetary colony to specialize in Industry, Technology, Agriculture or a mix of the three, depending on the type of planet. Industry could increase all build rates and slightly Lower all additional build costs at that planet, Technology would slightly speed up research rates, and Agriculture would increase trade at that planet and slightly further increase population caps. For Example with a Terran world (4 upgrades in this category) you could have 2 Industry upgrades, 1 Technology upgrade and 1 Agriculture upgrade or you can choose to only buff one of the choices. However with a Volcanic World you can only choose between Industry and Technology. This is just a quickly thought up example, I'm sure the developers could balance this better than I can.
Another example would be for the Upgrade Logistics Capacity. Last I checked all the logistical structures either cost 0 or 4 logistical spots, so I would propose some variations there.
2) Unpredictable natural events.
Just to keep players on their toes really.
I would love to see occasional natural disasters that would randomly harm your planets. For example for a Volcanic Planet your colony may spontaneously suffer from a super-massive volcanic eruption that would destroy a random percentage of your infrastructure and population count.
There should be a range of disasters, from floods to asteroid impacts, all with varying damage percentages where a flood would be anywhere from 1-20% and an asteroid impact would be anywhere from 60-95%, certain disasters should be particular to a planet type (no Hurricanes on a Desert Planet), and some should only result from your planetary upgrades (for example having more agriculture upgrades would lead to more frequent droughts, where not having enough would lead to more frequent famines)
3) More planet types.
Quite simple really. More variety = More fun.
Examples: Water Planet, Jungle/Forrest Planet, Atmosphere-less Planet etc.
4) More Sabotage.
TEC does this already with Rebel attacks, and all races can overtake a planet through culture, but I think there should be more ways to indirectly harm the enemy, or ally. I think this can be done through culture or diplomacy upgrades. Sabotage can be broken up either into events that harm a specific planet,events that harm the empire, or ones that harm the fleet.
Some Examples could be:
Planetary Sabotage: Terrorist attacks to destroy/harm/disable logistical or tactical structures
Inter-Planetary Sabotage: Synthetic Plagues implanted on trade ships to attack multiple planet's populations and can only be stopped by suspending trade and researching a cure.
Fleet Sabotage: An "inside-man" periodically reveals the location of his vessel and the composition of the fleet he is a part of.
5) More Everything Else.
More upgrades/higher upgrade tiers
More fleet capacity
More ways to make income
More ship abilities (every vessel should have some kind of ability)