Costacurta finished his Milan career in 2007, Maldini in 2009, 2005/06 was the last time Nesta played over 40 games in a season.
In spite of their great defenders/midfielders declining and not being reliable due to injuries, from 2005 to 2015/16 every time Milan spent anything over 10m euros, it was for an attacker, mostly CFs. In 2005 Milans big signing was Gilardino, in 2006 Ricardo Oliveira, in 2007 Pato, 2008 Ronaldinho, 2009 Huntelaar, 2010 Robinho, 2011 Ibra and ElSha, 2012 Balotelli and Pazzini, 2013 Matri. 2015/16 was the first time in a decade Milan spent anything noteworthy signing a defender and midfielder in Romagnoli and Bertolacci. And even then they continued spending their not so large amounts of available cash on Bacca, Destro, Luiz Adriano, Lapadula..
Knowing how most of those attackers turned out, this list is even more glorious

I'm not sure I'd be able to pick the biggest flop between Gilardino, Oliveira, Huntelaar, Robinho, Matri, Pazzini, Destro..