It seems like every unexplored system has a pirate fleet that wipes the floor with me. I tried starting a new game with "Marauders Off", and ran into the same situation. Are marauders the same as pirates, and if not, what's the difference?
That aren't marauders. Those pirates that you're encountering are just protecting the planets. Use your flagship to clear planets from them.
Marauders are wandering pirates that usually attack the player with the highest bounty on his head. In the late game they can be quite aggressive and plenty.
The capitol ship at the beginning starts at level 3, but until you research more there are only 3 upgrades available. Where's the choice here? Why not just start with those three, rather than make the player fiddle around activating them. Maybe I'm missing something
The abilities of capital ships don't need any research. You can chose an ability more then once, which makes it stronger. I, for example, prefer to chose twice the gauss blast and once the adabtive shielding. The gauss for the damage, the shielding for not getting any hull damage from those pirates.
Also, I don't care for the color schemes for "space". It seems odd to me to find pastel blues and oranges surrounding the planets. Maybe that's just me, but it sort of lessens the immersion facto.
You can turn them off in the options menu, effects submenu.