I have to disagree, I think the fleet supply system is one of the best things about the game. If the upkeep lowered automatically, there would be no serious disadvantage to getting your fleets destroyed, so long as you could rebuild by the time enemies came - people would incessantly raid instead of playing more carefully. The current system allows for gambits where you purposefully maintain a smaller fleet than an enemy player, using your relatively more powerful economy to get ahead in research and stock up money to build a big fleet later.
Tony_T: In practise, you can never raise a large fleet in a realistic timeframe if your upkeep is high.
Astax: If you don't fight when you can't win, you may lose planets, and see your own infrastructure whittled down, which leads to your ultimate demise. Meaning the system works precisely as intended; if you have fewer ships than your foe and less upkeep, you could afford to lose part of your fleet in return for damaging his because the cost in relative terms to him is greater.