Well here's my two cents. First off I have to say that I love this game, and will continue to love it for years to come. Now, a few minor suggestions that I think will improve the flavor of the game.
*I'd really like to see more control over the Galactic Senate, such as the ability for the player to call a meeting of the Senate and propose laws from a list that would be beneficial to ones own empire or to others. This way influence will play a greater role in the overall stratagy of the player. To make this more interesting the player would have to research a tech such as "Galactic Law" before being given the ability to call meetings and propose laws. Some laws could be trade embargos against a race, being banned from the senate, no race being able to declare war on another senate member with out full backing of the senate, and finally a law prohibiting or promoting all out wars with the minor races.
*More penalties associated when losing control of your domestic government. Such as having the controling party override descisions such as wars and making peace with your enemies, by giving up tech or money behind your back. Or if the war party is in power they might decided to attack an ally or steal tech from friendly races. Government types such as Star Federation should be opposed to war and have planets defect if a war is sustained for long periods of time. But only if the war is engaged by the player not if the player is attacked or fullfiling alliance obligations.
*More options for espionage, being given the options to steal tech, destroy buildings, use nuclear/biological devices to destroy planet populations. These options should only be made available when you've researched the right tech, and when you've spent enough money on espionage and have infiltraited the enemy races top levels of government and military.
*Planatary bombardment screen would be nice window dressing for those who like that extra special touch a mushroom cloud brings to a planet surface.
*Finally, more movement points for Terror Stars and more penalties for building them, such as having trade embargos placed on you, expulsion from the Galactic Senate...
Thanks for your time, and thanks for a wonderful game!
~SDC~