I remember Mike's article on the advanced Gemini otherwise known as the Big Gemini from the May 15th that was well written. A capsule concept from the little known past that could have been where apollo was on that date 35 yrs ago.
I agree that the first step in any rocket design is the capsule since it plays not only the role for Launch but also for return. It is the first of many blocks in a modular design approach. This is how the Saturn V was done as well.

We had capsules 35 years ago. The space shuttle moved us beyond capsules 20 years ago. We need to forget the moon and focus on building a new totally reusable spacecraft that can achieve earth orbit. It should be cost effective and reliable. From there we should design a platform to go to the moon. Not before!

The Lockheed lifting body concept looks capsule-like to me. Somewhat like the winged gemini proposal.
http://www.astronautix.com/craft/winemini.htm
This design falls somewhere between a capsule and lifting body.

I guess that the different types of CEV will be more alike at a system and componant level rather than from their outside shape.

One could say using a Delta or Atlas derivative is also the way to go but much like the shuttle derivatives is it economical since neither is a man rated vehicle to start with. Only the shuttle hardware is at this point.

In either case the question is where is the cash for developement going to come from under a squashed budget?
What is the timeline to manned flight?

Enough said about the rocket lets talk about the most important place on the rocket which houses the crew. Now depending on the launch format(winged or capsule) and the return re-entry landing style everything else is about size of crew, duration of use and easy of use to inside space demensioning.
Everthing else that is needed is an add on module and or boosters for each stage.

Now lets not forget the reason why we are in this situation in the first place.
Foam that sheds on launch from the external tank that could and does strike the orbitor. Not fixed as of yet but being worked on for return to flight.
No escape abort of launch if severly damaged since unit did not have real time broadcast of data though it had recorded the damaging strike. Note this is one of the fixes for return to flight with leading edge sensors.
If a strike does make a hole no means for repair was possible while in orbit. Last I checked they where still working on hole size variety of patch capability.
This also introduced the need for safe haven retreat or secondary shuttle rescue launch if unrepairable.

Now with those things said some of these things could be difficult even under a clean slate design to resolve.

Hi...I would say ..Stick to what works....Refine the Apollo capsule..fit it with modern electronics and computers....man-rate the Delta 4 Heavy;going to a Delta 4 Super Heavy with 4 liquid strap-on boosters....stack it all up with an escape tower...and go for the Moon....Now this is all feasable..Look what the Chinese did to the Soyuz.. The interior with all its modern displays etc,looks like something from Star Trek!!!Refine the Apollo capsule,make it larger and more robust....I believe that it can be accomplish...We have the knowhow,the vision is there,the public support is there..Lets get going and stick to one thing at a time..The Moon...Mars......and beyond....Jake

How's that?

If you went ot a capsule it wouldn't matter if the rocket shed foam. The capsule is on top.
The issues you listed are all part of the same problem & have been solved already with previous designs.
If one simple leason is to be learned would be to put the capsule, shuttle, etc on top of the stack
in future designs.

CEV design -- smaller is better

I would like to touch upon one issue of the design of the Constellation, that of crew size. I think a crew size of two is best. A CEV of minimum size maximizes operational flexibility and crew safety. Please hear out my reasons before dismissing this idea.

A CEV of minimum mass can use a booster of smaller size than otherwise. A smaller booster will fly more often than a larger booster, increasing flight experience which translates into increased flight safety. If the CEV is the same mass as the old Gemini, than a Delta II class booster such as the SpaceX Falcon V could launch it to an ISS rendevous orbit.

Operational flexibility is superior with a small crew vehicle. More missions will require only a small crew than a large one. It is easier to launch mutliple smaller rockets when needed for a big mission than to launch one big rocket for all small missions.

One example of superior flexibility is in keeping one launch vehicle available with a high alert rate for emergency purposes. This is much more practical with a small CEV.