edit:
> 1. Gentle delivery of large modules for attachment to existing complexes. - Probably lost, the main reason the shuttle is gentle is because it carries fragile humans.
I cannot imagine we don't have any launcher that can do that. Any launcher, when approaching its payload limit, should be very gentle (as in pull low G's). A Saturn V was much gentler than the SRBs in terms of vibration, BTW.
> 2. Bringing cargo down gently. - Partially lost: the cargo bay is much smaller.
How many times did we need that? We could keep one shuttle operational for that kind of mission or just build a bus-sized capsule that would go up empty and land on parachutes.
> 3. Safe "proximity operations." - Lost or at least made much more challenging.
I am not sure I see a scenario where we would need that. The arms attached to the station are adequate for manipulating objects close to it and capable of doing it very precisely. Automated cargo vehicles have been servicing space stations for decades.
> 4. Temporary deployment of a workbench in orbit for experiments, repairs, and other assembly. - Lost.
Do we really gain so much by bringing the workbench back? Why would "temporary" be an advantage here? Couldn't we just pack the supplies and leave the workbench there?
> 6. Flexibility of crew composition. - Lost.
We could have built a larger Apollo capable of launching 7 people. For a fraction of the price, most likely. If putting people in LEO were cheaper (a promise the shuttle never fulfilled) we would have far more diverse crews in space.
And all of that negates the fact the shuttle is useless for anything beyond LEO. And LEO is costly because we have to take everything with us.