I think that penalising the player for minimising the 'boring bits' is an unusual (and questionable) game design strategy. So if there's to be no penalty then the question becomes why aren't the non-players doing it too?
One thing I failed to mention in my '1 sentence' answer to cbr is that we want to avoid the tedium without also avoiding the 'action'. The action is more exciting when it's surprising and unpredictable, not when it's mundane. So we need those trader encounters but it would just be nice if they didn't take so long to resolve.
The problem of long distances (wp-sun, wp-second planet etc.) remains.
I'm considering in-system hyperjumps ("hyperleaps"?)
I personally don't find torusing to other planets/suns boring - I see the planet slowly looming larger as I approach, there is a sense of speed, of distance, of progress.
I don't find manual docking boring (although I do like the option of using the docking computers) - I hear all of the system coms, against a backdrop of station and planet, and I'm involved in skill based procedure that will be rewarded if completed successfully.
I didn't even find mass-lock boring in elite - 'I wonder what ship that is passing by... another python, there it goes'.
Atmospheric, scenic, progressive. Overtaking an inbound mass-lock however is none of those things, well maybe one, if you're being generous.
'Hyperleaps' could be fun though.
Obviously when everyone has torus drive, no trader will stick to the lane if there's any chance of a pirate encounter. So pirates will go where the traders are: near the witchpoint (and to a lesser extent any trading stations). Not too close because that makes them easy prey for cops or bounty hunters, but instead of packs strung out along the lane, you'd have a loose 'shell' of groups around the witchpoint.
...until (if you extrapolate further) the lane becomes the optimal route to take, and so the traders return, and so the centre of those 'shells' become the most guarded and so the pirates position themselves along the lanes rather than just the at ends, until the police patrol the lanes, etc. etc. etc.
The appeal of the lane is that it has the shortest distance. Unless I'm getting myself confused (quite possible) an optimal strategy, where there is free movement of all parties, would be one where the distance from the lane was as little as necessary to avoid significant increase of risk and no further
. Thus the lane will likely always have a pull of sorts to the extent that traffic generally would not likely stray too far from it.
Meanwhile, back on ship roles...
After having an initial look at the weighting idea, I can happily shave about 0.03 from the average speed of the typical trader, courier & smuggler. That might not sound like much but consider that aegidian granted the player ship a bonus of only 0.05 in an attempt to remedy the same issue (IIRC). The 0.03 benefit would be to ALL player ships however and not just the MkIII.
If I can get the benefit up to 0.05 and still have a plausible weighting then I think I'll be happy with that.