You can change the max fleet size at starting..
1. open my computer
2. open c:\Program Files\Steam (or where ever you steam folder is)
3. open steamapps\common\Endless Space\Public\Simulation (your directory should now be: C:\Program Files (x86)\Steam\steamapps\common\Endless Space\Public\Simulation)
4. Hope that you have installed Notepad++, if you haven't wordpad works too
5. Open EmpireDescriptor.xml
6. Find Line:
Set this value to anything you want, it's recommended to stay under 40.
then you start with the ammount you set and get the "extra" through research..
I have not found how to increase the ships via editing the research xml.
Step 6: Find Line:
What line?