You previously mentioned a puzzle style mission system where each puzzle is hand crafted such as pirates needing to be killed, cargo transported, leading to the entire economy being affected. Will it be cut and dry, kill pirates, find the wine, loot it? If so how is it going? If not, what's planned?

There's your generic mission lines that while they're awesome, once you've done it, you've seen it all. Tony's logic is everything around you can be a mission in a way. If you're on a planet with a refinery and there's an asteroid belt nearby, you'll see freighters going to and from that belt, and you can help or you could destroy or board some of those freighters, loot them.