Charlie, I'm sure that ASA management tell controllers that the system is broken because airlines/ industry want it that way, just as airline managers tell us line drivers that "ASA is heavily unionised and controllers won't change their practices". The truth may be a little from column A and column B but the fact remains that a 10 minute delay at 200 miles or less (common example) is not "absorbing all delay at cruise altitude"; but rather losing time on descent which whilst doable, is a major pain in the @rse in terms of energy management and efficiency.
You ask "How do you flow a sequence with aircraft that aren't airborne yet"?
Given that most traffic into capital primary's are RPT with a known schedule; I'd ask why cant you?