The point is adding more survivavibility to the player if he takes a severe hit, because he gets to pay less upkeep, thus having more money to rebuild.
Which is precisely why it isn't going to happen.
The goal behind the upkeep system is to make the player manage his fleets carefully, and not just keep pumping out hundreds of ships like more conventional RTS games (see SupCom).
Fleets are made to be managed, not carelessly thrown away. If you make the upkeep system be per-ship or equivalent, a big enough empire can just afford to spam ships ad nauseum since money and resources never run out, and when they drop to low upkeep they'll be raking in huge amounts of money.
The way it is now is that fleet sizes and upkeep scale to the size of your empire. If you have a big empire, you can afford to lose a lot of ships and still be making enough money post-upkeep to afford to rebuild. If you have a small empire and lose your maxed out fleet, of course the upkeep is going to eat you alive when you try to rebuild because a small empire isn't meant to support a huge fleet.
Edit: Oh, and please don't call people who've been on these forums for a very, very long time fools - most of them actually know something, and Hack78 is quite right.
