Imagine trying to service the Hubble from a capsule. I'm not saying it couldn't be done, but it would be much harder than from the bay of the shuttle. What I think we need is an all around system, one that can be configured to do a wide range of tasks.

A Buran type shuttle is what I have in mind. Take the main engines off of the shuttle and place them underneath the ET, then enlarge the ET so that it can carry more fuel, thus more weight into orbit. By doing this, you have in effect created two vehicles, a manned orbiter and a heavy lift unmanned launcher.

The heavy lift launcher could be used to place 100+ ton payloads into orbit when not piggy backing the shuttle. The orbiter could also be fitted with jet engines to give it atmospheric flight capabilities, allowing it greater flexability during landing.

Space Island Group seems to have a pretty good idea on how to run a space program.