This is a great discussion!
First, regarding the possibility of negative income, I would like to draw attention to Gaien Crescent, for those that doubt the possibility of true negative income - in fact, the beginning of the game you have negative income. The map requires decisions of whether to make your initial planet your Cap home world (thru the upgrade), create an economy on your planet, or build a missionary or military excursion. This example can be experienced by everyone who owns the game in less than five minutes. This crushes the issue, because it IS real. In fact, if you make the wrong decisions on this map, you will literally be at 0 credits, with nothing to show for it, until someone comes along and kills you!
On the subject of huge maps and economies of scale... I've played Areolian all the way through, Huge Random several times, and I see end game as a graceful game of chess on huge maps. If you want to make several extremely powerful fleets, then so be it. That may be end up a smart decision, or you may regret it later on. There is nothing cut in stone about how a fight will turn out "by the looks of things." Micro management, economical manangement, and fleet capacity all weave together to form situations that each player will face with different tactics and perspectives. You can predict a lot of events unfolding in Sins, but you cannot determine the outcome by a simple number crunch.
If you aren't making money, then you obviously need to evaluate your economy, and adjust your strategy accordingly.
When end game draws near, I rely upon one of my main rules of thumb of RTS - it will not be a flawless victory. There are split second decisions that you will make as leader of your empire that will ultimately make positive and negative impacts on everything you control. Nothing will be perfect. Sometimes, you need to take that enemy planet on the front line. You know he's going to counter with a smaller force on one of your flanks. This is war. People are dying. Keep reminding yourself that not every shiny new defense laser pew pew beam is going to maintain a flawless record against your enemies. It may get owned. Your planets may take a lot of heat, and your armies may need to be constantly remade and retooled as the game plays out.
The game, as highlighted by the fleet cap, has several physical limitations and ceilings in place not only because of necessity of concrete game dynamics, but also because of PC specs. It's a game people, it's not the actual complexity of running a true real life empire. Analogies are great and everything, number crunching has its merits, but the fact remains that the developers are always striving for the most balanced game that gives all players of different styles and capabilities a chance. Giving a player a chance does not mean they deserve to win. It means they deserve a level playing field with many different strategies that can be used, all towards the ultimate goal of winning. Some games you can win without even losing a single ship. Some games, you will be teetering on the edge of existance, and an unorthodox decision in a critical moment may ultimately swing the tide in your favor, maybe even giving you momentum for the rest of the game. Smaller empires do deserve a chance, but not because they are n00bs. Because it's legitimate, it is for real, it is the reason we play these games - upsets happen. It's the quintessential Rudy, the Rocky inside all of us that we want to see come out, digging deep, and finding what it takes to fight off the big guy.
Rome fell. Then again, it's still around...
On the concept of ganks, it's ironic that most of the rebuttals have hinged on a situation arising in which several smaller empires gang up on the largest empire. There is diplomacy in this game. Even if it is some form of co-op, or a single player game, you have the chance to deal with other empires in ways that don't involve fighting. Just throwing that out there.
Considering the earlier allusion to chess I made, take it at face value. My perspective on end game, with particular emphasis on larger maps, the fact remains that there are different strategies that one can use in order to "finish off" the game. It's not over until it's over. I'd be willing to bet on the bigger empire, regardless of the fleet cap. I wouldn't put all my eggs in one basket, however. The reason we even play the game is the unknown outcome, if it was decided by simple numbers and exploitive strategies, the games would become more scripted.
PS - Yes, I'm saying the fleet cap is (pretty much) fine. I don't think Sins was designed specifically for people to only play huge modded maps w/ triple digit planets, who want to raise the fleet cap so they can get the exact same battles with twice as many ships (and CPU load). I understand the difficulties of expansion due to the fleet cap on huge levels; I believe it is a strategical hedge, intended to induce exactly these types of situations a commander faces, in regards to logistics and mobility. Also, I haven't seen much talk regarding the amount of skill a player has with regards to micro management finesse, in a game [theoretically] dealing with 10000 fleet cap - I don't want to see Sins turn into some sort of uber-Starcraft. I respect that playstyle, I find it fun as well, but I don't think Sins is aiming for JUST that. It's already epic scale...