A lot of replies to go through, so I don't know if I missed anything or what, but here goes. Also I will try and put what type of thing each one is about. Sorry if any of this has already been said.
STARBASES:
Make the number of starbases buildable in a sector controlled by techs, so that you can limit them and if the modder wants even make a hard limit.
Make the SB maintenance moddifiable, it should have maintenance btw, but also techs that allow you to lower the maintenance through time, and even improvements or wonders that allow you to lower them in the sector or all over, the wonder could even remove the maintenance cost.
A SB module that allows you to trasport ships in that sector instantly to anyother starbase of yours that also has that module...unless this exists and I missed it.
RACIAL TRAITS:
Make the Yellow star visibility a racial trait. Why do all of the racial traits have ot be a bonus? Can't we have some things that are just special, and not just a bonus.
GAME SETUP:
A setting when setting up the game to control the rarity of Anomolies, Random Events, and Planetary Events, all separately if possible.
SHIP HULLS:
Allow certain specials on a hull. For instance makea certain hulltype stealthy (can only get it after a certain tech of course), make them a bit more unique, so it isn't always biggest is best.
A command ship type function, reduces the influence of other empires in the sector it resides in. Maybe even local sector governors that can do that, they have a different rating that helps control influence and counter-influence.
TERROR STARS:
Allow us to edit terror stars, and alter the default races starting stats
COLONIZATION:
Allow the modder to control the effect of colonizing planets below 15, maybe even incrememntal steps to allow for better control and technological advancement. Say 11-14 have a certain impact unless XXXX tech is researched, 7-10 this impact until XXXX2 tech is discovered, and so on. Maybe make it based on the star, and have the star type have a greater effect of planet type in that system. Or even make it based on the planet type itself.
SHIP ORDERS:
Allow us to give preset (customized) orders to ships in queues(Colonize immediately [auto-colonize], protect planet, join largest fleet, protect front lines…)
Allow an autocolonize setting which sends the colony ship to the nearest known yellow star.
Allow ships to go on an interdiction mission. Meaning anytime a non-allied ship enters your area they automatically move to intercept.
SHIP UPGRADES:
I hate to suggest this, but do not allow ships to upgrade unless they are in a sector with a planet of yours or a starbase of yours.
SHIP WARNINGS:
Some sort of warning when an alien ship enters any area you can see or detect them in...some sort of notice. Maybe give all hull-types a stealth rating that affords them a chance to avoid detection on a per turn and per parsec basis. The closer you get the harder to avoid, other techs could also allow you to do detect them easier. Doesn't have to be a percentage number, make it some how the higher the stealth over the detection rating the better chance of avoiding detection. Make it a sector by sector rating or something like that.
DIPLOMACY:
better diplomacy ability for alliance interaction during war for planning.. and be able to ask another race to please stop your war with my ally and friend.. maybe be able to pay them off.. this would allow possibe another victory condition
Allies can use joint attack and joint defend. They can be asked to defend certain sectors as well. But vice versa as well.
RESOURCES:
More resources, or a way to add our own (those that you build SBs on)
SLAVERY:
Not sure how slavery works yet, but is there a way to liberate or help liberate them?
EVENTS/ANOMOLIES:
More possibilities for events, anomolies and UP events. Maybe even make some events not be a choice of what to do. EX: Your ship mysteriously exploded. Or your planet discovered a strange fungy that enhances its quality. Not everything in life is a good/evil decision. Of course I never tried it without the usual options so it may work, I don't know.
GOVERNMENTS:
More government types (not parties) and a better definition of what they do. Not sure if we can alter them and add some, but if we can't open that up as well.
~SDC~