I'm certain it's been noted already, but the Shuttle was a necessary system with respect to production and technical implementation in its own time. Obsolete now? Definitely. But realize you're bashing a 30 year old space plane. The argument that "other old flight systems which are of a similar age or older still function well, yet..." doesn't apply, as space flight is still a very immature field in aerospace. The Shuttle, again, was necessary for the evolution of spaceflight.
Now, were there better design solutions available? I think so - a lifting body configuration would have been the best configuration for this type of flight system in my opinion. But realize that ANY vertically launched space flight system is going to be inherently inefficient. Basically, if you were going to build a new shuttle today that launched nose-first into the air from the ground, you'd still have boosters and fuel tanks - there's no way around that due to the available conventional propulsion sources. Skylon gets away from this as - imagine that - you've got a new powerplant. Leave the Shuttle out of this.