It seems there were individuals responsible for ensuring this 'systemic failure'.
You're talking a LIHOP scenario. The LIHOP scenario in which someone(s) intentionally allow the system to decay over decades would involve probably more people than any other 9/11 "inside job" theory I can imagine.
It's important to remember; prior to 9/11 Americans did not consider terrorism a serious threat. Soviet Russia was seen as the last great threat to the American mainland, and with the end of the Cold War many felt America was going to sail off into some eternal sunset of global supremacy. Every layer of protection you can imagine was stripped back, revoked, had funding pulled, and was allowed to atrophy.
If we take a single example I'm familiar with - air defense - during the Cold War NORAD had hundreds and hundreds of armed fighters ready to scramble at a moment's notice. They had multiple long rang radar lines across the north of Canada, they had naval surveillance ships held in permanent picket lines off the coast, they maintained a constant airborne surveillance presence...
But over the 90's these numbers were halved and halved again... NORAD's budget was slashed repeatedly. Projects to replace their fighters with newer craft were delayed repeatedly, with final numbers constantly reduced. NORAD's internal systems weren't upgraded, and the gap between their equipment and the FAA's grew increasingly wider until their systems were so different they couldn't even talk to each other.
What's most frightening to consider about air defense is not how bad it was, but that it could have been even worse. Consider...
In 1994 it was recommended that the entire air defense mission was scrapped. You would have had NO armed fighters on standby anywhere in the USA.
Also consider, during the mid 90's the FAA started investigating the impact of ceasing all Primary Radar Surveillance in the United States, and found the impact to be "negligible". A few months before 9/11 the FAA were in the process of beginning the project to turn off all Primary Radars. Only the protests of the military saw it slowed, and the FAA were basically saying if the military wanted them, they'd have to pay to keep them running (something the military didn't have the budget for).
So let's revisit 9/11, but with no armed fighters on standby, and no primary radar coverage. Certainly the end result would have been the same in each case, but can you even imagine the chaos that this would have created in the aftermath of the attacks, with thousands of aircraft trying to land?
As it was, it was difficult for the FAA and NORAD to get a handle on what was happening.