Turning off certain ship types disables them for both you and the AI, so you won't have to worry about them using fancy tools that you can't get. Simple should be fine for a learning game where you don't want to have to check references every 5 minutes to figure out what the heck that new ship is. There's not anything I can think of that the AI might have that you have to have normal or complex ships to deal with. There are plenty of tools in your arsenal any way you set it up.
Core shield gens were really only put in to keep people from short-cutting most of the game and aiming straight for the AI homeworlds, so with or without them you shouldn't have much trouble.
I would suggest against turning off cloaking, thus disabling scouts, even with complete visibility on. The reasoning being that scouting is a sizable part of the game, and turning that off just doesn't seem right. I always feel like I've done a good job and passed a milestone in my games when I finally manage to scout out the entire galaxy. And for a game where you're trying NOT to get overwhelmed, starting out with visibility on the entire galaxy is a bad idea, in my opinion. Scouting nearby planets and finding those goals that are in range gives you bite-sized bits of gameplay to shoot for. Once you get to the first planet with something good on it, then you scout out again for the next one and so on. Seeing it all from the start would just make me feel like I had too many options and I wouldn't know what to shoot for.
That said, the reason there are so many options is that there is no 'right' way to play the game, except for the one that works best for you. So take all that with a grain of salt and go with what you enjoy.