If you guys are brand new to the game then I suggest you play through the in game tutorials to get acquainted with everything.
With regards to customization, the game is very granular. You can turn on/off entire expansions, types of ships, factions, and ai behaviors. If you want to just jump into a game then you should just play against the "vanilla" ai type with everything under AI Plots and AI Options tabs set to off. There are some things there that are just an advantage with little to no downsides, but having everything off would make for the least complicated game.
Don't worry too much about the difficulty. There are like 15 or something difficulties that gradually ramp up the pain. You can set it up so that the ai is morally opposed to harming you, or so that you lose in 5 minutes. For a first time game, it's really up to you. Difficulty 7 is "normal", but I find it pretty challenging. Maybe you would want to start on 5 or less?