The Nationals were an aging team without a real chance of remaining a contender. The 2nd half of 2005 season showed that. So the Nationals went for draft picks to go along with Ryan Zimmerman
You're deluding yourself if you think they fixed any of that in 2006. A rotation with Pedro Astacio and Ramon Ortiz didn't address that problem.
Bowden put together those awful teams from 06-09, and the Lerners didn't bother firing him.