Typically, I only build up a military when I need it. I keep my coffers very full and my designs up to date so when an enemy challenges me it takes me just a few weeks to draw up a good-sized fleet with the best technology available, usually more than enough to pummel my would-be conquerors into submission. However, once I have all these ships they're taking up a huge portion of my income in their upkeep and if I decommission them I only get pennies on the dollar returned. I know it's a balancing act but I have another idea...
Most other nations with any warships at all will start to hate me just because they're superior to my free-standing armada. I don't think every single nation should have such a strong desire to conquer, or should at least take into account another race's military potential. Sure I don't have star destroyers floating around their home planet... but give me a week or two and I could. I'm tired of having people declare war on me just because I'm not belligerent. I've even tried using frequent trade and gifts to keep them from attacking but no matter how good of friends we are, no matter how beneficial it is for them to leave us alone, eventually we're always attacked.
It'd also be nice if we could mothball old ships without destroying them entirely. A stored ship could require a week to activate and take damage over time (to simulate disrepair), but could only cost a fraction of the usual upkeep. That would allow peaceful nations like me to keep ships on hand without paying as much for them as would a race in the midst of an all-out war. Or at least decrease the cost to maintain ships that aren't repairing/rearming that week...
Greater accessibility to planetary defenses might be nice too. It'd be cool if we could treat planets, even unhospitable ones, like starbases and upgrade them with orbital platforms. Maybe we could even get a terraforming module to improve the quality of the host planet, thereby allowing us to populate unhospitable planets as long as we're willing to put forth the investment.