I like taking my time finding every crumb of minerals and crates/lost packs. Aquarq missions give me ulcers with the constant stream of enemies when you're in it for too long. I think my favourite is regular ol' mining missions. Usually just a single tunnel, easier to see it all along the way.
Yeah I do wish mission control would warn you that Point Extraction gets worse the longer you stay. I was a hundred hours in the game before I found out from a random person I was playing with.