You can disable the crew limitations also you can have multiple ships. I usually play with one factory(for mining and processing), one starbase (a gigantic storage, waaay bigger than the ones from the game) some smaller ships for defense and quick intervention(often nuke carriers) amd one or two really big and heavily armored Fighters (record enemy destruction was 0,5seconds with a 20 rail guns offensive)

Most things you complain about can be changed in the options or with simple mods, you don't even need to mine, you can just buy stuff. Also capturing enemy ships is unnecessary for farming, just drag the mine tool over it (or install a mod that lets you harvest them for no resource penalty)

The higher level systems aren't that hard, you just need to upgrade your ship and larn how to combat with them, every ship plays different. Best way to survive is to outrange the enemy and be fast backwards to keep distance. (rail guns and rockets or lasers or everything)