Regarding minefields, I'd generally prefer that they not exist, as the number of mines required to meaningfully limit safe passage through a region of space is excessive even if we're just talking about mining the orbital space around a planet. Jump points might possibly be reasonable if ships can only enter or emerge from them in a very, very small region of space, but unless the point is associated with a nearby large body you'd require station-keeping thrusters on all the mines, which raises the cost and increases their visibility, reducing the effectiveness of the mines.
Regarding the fleet 'contrails' - is there any chance that we could have these linger for a while, in some fashion, so that we could have a way to track fleets? Might make the named bounties more interesting - the "rumors that so-and-so hangs out near XYZ" would only need to get you close enough to the target soon enough to pick up the trail, and you could follow it towards where the target is rather than always finding the target at wherever XYZ is.
Regarding asteroid belts - would it be possible to asteroid fields in addition (as a harsher version) or instead, or as an occasional feature of ring systems? Something that indicates "something big used to be here and was destroyed by some catastrophic event but the pieces haven't had enough time to drift apart enough to form a belt" or "something big is beginning to form here but hasn't really coalesced yet."
Regarding the fuel generation in nebulae - starship fuel in Starsector explicitly contains antimatter, and it's strongly implied that the facilities to produce antimatter and package it into fuel are sufficiently uncommon that it's not likely that ships would carry antimatter fuel production plants. It's an interesting idea, but I think not really one that fits the base game's lore. I could see collecting volatiles from nebulae or gas giants, but that's probably too much of a repetitive timesink, much like manual mining.