One of Aikman's best seasons was 1998 at the age of 32 when he no longer had Novacek, Harper, Stepnoski, and Tuinei. Three out of four were Pro Bowlers. His productivity declined at the same time the team's talent level declined, the guys that replace those four were mostly busts like David Lafleur and Clay Shiver or non-productive free agents like Billy Davis and Jeff Ogden.
He lost Irvin, Johnston and Newton in 1999, all three All-Pros. Their replacements were not exactly household names.
By the time Troy Aikman retired in 2000, Emmitt was the only offensive player that had shared three Super Bowl championships with him.
Aikman was never part of the problem, that offense was systematically destroyed by Jerry Jones's failure as a GM to adapt to free agency as well as being a putrid talent evaluator.