Shanahan didn't draft his great teams, he got them via FA. In those days few teams were competing for FAs since it was new and lots of teams insisted on drafting and developing their own players instead of paying established veterans. Shanahan was able to sign HOF LT Gary Zimmer, pass rushing DE Neil Smith, and LB Big Alfred Williams, FAs like Tony Jones, Ed McCaffrey, etc., etc. Today doing that would bust the bank. No team could afford it.
When his original players aged and retired Shanahan was unable to find equal quality replacements in FA because other teams were competing with him and driving up the prices, and because the team was mediocre, so penalized to always pick in the middle of the draft. He failed spectacularly with various picks too which hastened his departure. But, his biggest failure was the failure to draft a QB who was able to save his job.