Yes, I've posted about this in another thread. The current system lends itself to cheesy exploits far too easily at the moment. Basically, i think the upgrade sytem needs reforming. My idea was as follows:

Each turn, the player can work on a number of upgrades limited by his logistics ability (so one fleet's worth, basically). Ships in orbit around planets with shipyards or military starbases take 1 turn to upgrade; ships in a sector with a player planet take 2 turns; ships in a sector with no friendly planet take 3 turns with a +25% upgrade cost penalty; ships in a sector with enemy planets take +1 turn and a +25% upgrade cost penalty. Ships cannot move without cancelling the upgrade and writing off the upgrade cost, but ships can move/fight normally until it is their turn to start being upgraded, at which point they'll be parked, so you can issue a general upgrade order, but still be able to order active ships to return to base (see below). I think it is reasonable that ships are completely repaired after being upgraded. but I guess there's nothing wrong with adding to the upgrade cost... say 10BC per hitpoint repaired. It's a minor issue IMO.

The upgrade cost to be deducted when work starts on a ship, with players no longer able to go past -500BC of debt in order to pay for upgrades (this stops the cheesy tactic of being able to suddenly buy a huge superfleet), with ships entering the upgrade queue in ascending order of upgrade time (so ships that take 1 turn are started first, then ships that will take 2 turns, etc), and then in ascending order of hull size (so Tiny ships first, then Small ships, etc.).

So this system still allows the convenience of issuing a general "upgrade all" order, but without the exploit of suddenly creating an uber-fleet inside another player's border regardless of expense.