Never actually thought of that, but yea, I always found it kinda odd that the shopkeeper paid the delivery guy who was working for the supplier…
Things I've thought about pertaining to the overhaul:
Couriers will have to register with Bruce, putting them on his books as employees. This will be handled by code and there'll be pretty much no restriction, so -everyone- will still be able to do Bruce runs but they won't just be given to any anonymous Joe who walks in off the street. Known criminals or previously unreliable couriers will lose their registration with Bruce and not be able to renew it until certain criteria are met that satisfy him.
Possible idea: Instead of going to Bruce and asking for a job, job's will become available every so often and Bruce will broadcast the job details over SIC to all registered couriers. First courier to get to the warehouse will pick up the job. Yes, this will mean you need a SIC to do Bruce runs, but since Bruce is a legit business and the SIC is your social security/ID/citizenship/legal documents, Bruce is -very- unlikely to hire you if you don't have a SIC implant.
Crates won't contain 1 single object and jobs won't only be available when there's space in the stores. It's fair to assume the stores sell -far- more than the few coded objects the player base takes, so the crates will actually contain a whole load of stuff the store might normally sell. This 'stuff' won't be converted into objects since it's all basically just 'fluff'. Some deliveries will contain 'useful' objects that will be stocked to the shelves, but many deliveries will contain nothing of use to the players (tampons, newspapers and the million other things the stores can be assumed to be stocking.)
I intend to add code that will allow you to simply not bother delivering the crate and open it, taking the contents (if anything useful) for yourself. This will, of course, lose you favor with Bruce and possibly result in you losing your courier job. Enterprising criminals may also make a living of mugging Bruce's couriers and stealing the crates. Pilfer through the contents and steal anything 'good' you find. Alternatively, you could deliver them yourself to a 'fence' NPC who will pay for intercepted crates.
I pondered varying the weights of crates, rendering some only deliverable by people with vehicles or stupendously high strength. Maybe, maybe not.
The change to jobs becoming available every so often will also remove the limitation that currently means only one Bruce run can be in existence at any given time, killing the occasional bug where a crate gets lost in space and Bruce refuses to hand out any more jobs because of the 'in transit' crate.
Based off Jadael's idea about payment... yea, perhaps a receipt system so Bruce pays you when you return or maybe I'll have Bruce keep a tally and pay his workers at the end of each week or day or something.
Oh, and players with 'other jobs' will no longer be able to do Bruce runs. Bruce and SHI are meant as stop-gaps for characters without proper jobs. It gets pretty tiresome to see the few characters with paying jobs collecting their weekly salary for doing alot of dick all then doing Bruce runs and sitting in SHI all day/week/month. Bruce can actually be a -very- lucrative career choice, it's going to be severly unbalancing in the long run for salaried characters to bolster their bank balances with Bruce work.
Of course, don't expect all this to happen in the near future...