Well, I don't have the experience in this game that a lot of you seem to have, since I haven't the time to play as much. I mainly play on huge maps, but I haven't had an empire as large as the ones your referring to. I do question how much beta testing went into this aspect of the game, since most players, in my experience on other stratagy games such as Civilizations, prefer to play quicker, smaller games. How many of the beta testers actually tried to test marathon games that last for several days or even weeks with 100+ worlds to deal with?
Anyhow, here's an idea to run by you all. How well would it work if the current fleet upkeep system remained intact, but create a fleet cap that is scaled by the empire's economy. You would still pay a flat upkeep for the fleet whether you've built it or not, just like now, but you have the potential of building a much larger fleet if your economy is large enough. It would work like this:
Each ship has an upkeep of 1 credit/second, and for the purpose of this example, I'll ignore metal and crystal. First, calculate an empire's gross credit income. Then, deduct the empire's tax burden (income lost to corruption in the outer worlds) from that gross. Then, deduct the fleet upkeep cost from that net income (NOT THE GROSS). That is then your fleet cap.
Using the simple empires already being tossed around this thread, a small empire has 10 planets, each generating 10 credits/sec gross. They are fairly close knit, leaving a corruption loss of 10%. As such, before fleet upkeep, their net income is 90 credits/sec. Now, deduct fleet upkeep of 75%, which comes to 67.5 credits/sec. Since each ship has an upkeep of 1 credit/sec, that means this empire could field a fleet of 67 ships.
Now, the 40 planet empire has a total gross income of 400 credits/sec. However, due to their size, corruption is greater, loosing 30% of their gross income. That means the fleet upkeep cost is taken not from 400 credits, but from 280 (400 - 30% = 280) Now, 75% of 280 is 210. That is how many ships this empire can support.
The larger empire is 4 times the size of the smaller one, but can only support a fleet of about 3 times the size. Of course, this gets worse with larger empires still.
A very large empire with 100 planets at the same 10 credit income generates a gross of 1000 credits/sec. However, due to their very large size, 50% is lost to corruption (this is very possible when the vast majority of your colonies are below 50% alegience). As a result, they can only support a fleet of 75% of 500 credits, which is 425.
So, this very large empire is 10 times larger than the small one in the first example, but it can only support a fleet of a little more than 6 times the size of the smaller fleet. Also, the larger empire will be busy dealing with pirates, rebels, and other enemies attacking, meaning they cannot devote 100% of the fleet at the small empire. This drastically evens up the odds while still maintaining a larger empire's ability to effectively defend itself.
Now, in the event that you have 2 empires on the map, one with 10 planets, and the other with 100, then yes, the little guy is going to be at a disadvantage. Then again, shouldn't he be? He's fighting an empire that's 10 times his size - alone! The idea here is that 4 or 5 smaller empires could eventually beat the big one, but not easily. Also, remember this is based on economic power, not planets. If you have 10 highly profitable planets (like terran worlds), and your opponent has 20 lower profit planets (like desert worlds), then you'll likely be able to field at least as large a fleet, if not larger. Also, building lots of trade posts and such will ultimately increase your fleet potential, allowing a smaller empire the ability to somewhat keep up with the bigger juggernauts.
By leaving the actual expense deduction alone, you prevent the problem of a huge amount of resources building up to replace a fleet quickly. However, now you are actually paying the same for your ships, no matter how large or small your economy.
Of course, this needs some balancing. I don't know if the corruption rates listed here are at all accurate. I just chose some fairly arbitrary numbers based on what I've seen and read so far. Cost of each ship might need increased or decreased, and I would probably make certain ships more expensive than others (similar to how it is currently with the fleet resources).
What do you all think? I don't see anything like this being done officially, since the beta testers and developers obviously came to the conclusion that the current system is good. They obviously don't see the problem here. However, maybe something like this could be implemented in a mod in the future.