Something that will piss me off, as well probably lots of other, will be hardcoded limits to things. There is nothing more frustrating then that, for example Conquest: Frontier Wars, has been coded such that you can't get more than 200points worth of units, even with a special patch. I understand all the limitations of the game, but it would be REALLY COOL if you made the limit in a .ini file, so that in 5 years when we are running oct-core CPUs and 16GB RAM, we can play SINS with thousands of ships each player, simply by changing that value... Or when you release the expansion pack, or mod kit, or whatever, include the ability to make a "super-unit" mod...
Well, currently the hard fleet point cap is 2000, which could get you 300 or more ships depending on your fleet composition. This cap can be increased for single player, but not multiplayer in the same way you suggest, modifying a file

How it will be in release.. we will have to see

There was a big thread pushing the idea that the hard cap should be increased and multiplayer games should be able to pick from a few options (low/medium/high) as is fairly commonplace in MP games these days.