The Pirates have horrible management? Yeah, 15 straight losing seasons would be a good indicator that they are a bit deficient at putting a winning mix together. However, look at their last two big trades prior to this one, both executed under the same ownership.
Oliver Perez (2-10, 6.63) & Roberto Hernandez (2.93 in 43 relief IP) to the Mets for Xavier Nady (.264/.329/.487) - For an older, but performing well at the time, RP and struggling young starter who had one big breakout season, they get an established COF with decent power.
Mike Gonzalez (2.17, 24 SV in 54 IP) & Brent Lillibridge (light hitting CF-type prospect) to the Braves for Adam LaRoche (.285/.354/.561 with 32 HR) & Jamie Romak (.247/.369/.471 with 16 HR as a 20 y/o in A-ball)
They had already established a market value for Nady in 2006, and to their benefit, Nady had improved, going .278/.330/.476 with 20 HR in 2007, and was hitting .330/.383/.535 with 13 HR before the deadline in 2008. The market value was something greater than a young pitcher who had already had a breakout season and a good MRP.
They had already established a market value for a good LH closer, and to their benefit, there were no concerns about injury with Marte like there were for Gonzalez. The market value was an all-star level CIF (I consider the prospects a wash and throw-ins to the deal).
By the calculus established by the Pirates themselves, Nady and Marte were worth a promising young starter who had already broken out at the MLB level, a decent MRP, and an all-star level corner infielder. What did they get in return? Three AAAA fodder pitchers and a headcase 19 y/o COF with no power.
Not making any accusations, but there's meat on the bone if one wants to talk suspicious behavior there.