Wow, it has been a while.

Yes it takes a certain percentage out as you increase the level (from 9% t 75%)

It is the economic componet to the fleet size. You start out with 100 supply points and 0% taken out of your income for fleet mantinence, as you progress up the line more is taken out of your income as the fleet gets bigger until you reach 2000 supply points which takes out 75% of your income. If you are careful you can expand your fleet size properly. A 4 player/4 star map could easily handle going to maximum fleet size.

Yes most likely. I thought you had played a beta or something.

Entrenchment really fixes the problem you describe. You should try it only $10

if you control that much more territory than your opponents then the orbital structures based income you receive (from trade ports and resource refineries) should be immensely bigger than what your opponents receive. you ought to be able to leverage that economic advantage to buy more fleet upgrades than your opponent and maintain a bigger fleet on a permanent basis. 

the fleet logistics system in the game is designed to require you to expand your civilian economy at a rate proportional to your fleet size in order to maintain a constant income rate. you can build your income rate by expanding civilian but not military or you can expand military but sacrifice income. thats how the system is balanced. it works very well, even on large maps, once you've mastered getting the balance between civilian and military expansion. 

Hey summs.  I didn't know you'd ever played.

The base game is an extremely aggressive game.  It is heavily weighted towards playing manuever warfare over attrition warfare.  I'm not 100% convinced that was the initial intent of the game, but that's how it plays out.  Had I been in the situation you describe, I probably would have fortified the bejesus out of the conquered system with defensive structures and then not worried about it, using my fleet to bumrush one of the other AI, then sort of rinse and repeat.

Entrenchment on the other hand is awesome for setting up attrition style warfare.  Dropping 4 vasari starbases near the entry point from a phase lane is a great way to prevent somebody from jumping into your system with a devastating force.  As was said, you'd still need to get your fleet there, but you have a lot more time.  Anyway, if you're looking for a way to play defense then you'll need to play entrenchment, since defense in the base game is fairly nonexistant.

See you round.

That hardly seems worth the effort, especially if you intend to play online.  Maybe I misunderstand that you already have this mod and you're advertising it?

AI's dont run anymore unless they are obviously outmatched in the same grav well. they're pretty good at judging this too, its entirely reasonable. they actually will fight you now, its extremely different than the cowardly AI of Sins 1.0. aggressive AI behavior actually makes them slightly reckless as well, they'll try to attack from multiple flanks at once even if it means losing alot of their attackers. 

That was exactly my issue with the game at the time.