How about some environmental hazards (i mean, some real hazards)? Like the ones from those space rouge-likes (FTL, Everspace etc). Something that makes your playthrough less convenient but not necessary to destroy/shutdown to complete your objective (shield disruptors, sensor dampeners, you name it). We have some of those grineer mines, yes, but they do pretty much nothing (they could magnet to the ship at least; if they already do this - then they should be more aggressive with that).
Also, maybe some big resource deposits could spawn in missions from time to time (not as rarely as reinforced containers, but still rarely)? I know you've increased resource drops, but still.
Oh, and auto-roll is bad. It needs to be manual. 🙂
edit: a very good example of serious env. hazards - Sleeper Caches from Eve Online, those things make you sweat.