If at all possible I would like the ability to move minerals with civilian ships in the same manner that we can move installations I.e. set an amount for pickup/delivery. Mass drivers are great for intra-system mineral transport but it becomes tedious to transport minerals between systems - you have to rely on your own vessels for that. I think it is logical and consistent to give civilians the ability to transport minerals and it would alleviate some of the current micromanaging for larger empires. I would still build freighters for initial colonization and for restricted systems where I don’t want the civilians to go.
I think the last time this came up, the issue raised was how to configure the civilian AI so that the freighters aren't constantly running off to random rocks to pick up 25 tons of vendarite when you'd prefer them to ship 12,000 tons of gallicite from some important colony instead. One suggestion I made at the time was to give civilians a dedicated class of mineral haulers which are just small shuttles (say 5,000 tons capacity) instead of big hulking freighters, however this conflicts with the general trend to use larger ship types to reduce pathfinding/detection slowdown.
With the new colonist transport code, maybe something similar could be added for mineral shipping to resolve this, e.g., the payout for a mineral shipment is scaled by the fraction of the ship's hold that is filled, so civilians will only prefer to pick up minerals if there's enough of them to make a real profit.