You can mod the number of ships and supply points now, using a text editor in the entity file for the research for maxcapitalships and for maxshipslots for each race, the vasari, which are called the phase in the files, the advent which are the psi and the Tec, which are called Tec. 
Increase the numbers for basic, which is the first off the bat number you get with the first lab, and the next level numbers.
You can get the numbers how ever low or high you want them, and change costs high or low as you wish.
The problem i found, haha, when i dumped a ton of ships into my game was that i got overrun with these HUGE HUGE fleets,
haha, that and my framerate on my pc, which is only low end to begin with, just started draaaaaa-gggggggg-iiiiiiiii-nnnnnnn-gggggggg!! 
But you can always mix it up anyway you want and find something your 'puter will run. 
Talk to the modders!!

-Teal