Part of the reason this chain of command was both so complex and so ambiguous -- many officers involved in the operation later expressed confusion as to exactly who reported to whom, and where commands were originating -- was that General Frank of CENTCOM had strictly limited the amount of forward deployed command staff and resources he wanted moved to the Shahikot Valley (Grossman 2004; Lambeth 2005). Even without this forward deployed command, however, clearer and better publicized chains of command issuing directly from CENTCOM could have been created, or a single forward deployed coordinating and command unit could have been established. Both alternatives would have been more effective than the command system that was put into place, however haphazardly and unbeknownst to many officers even after the fact. Given the number of...

Secure positions were certainly available, and the area as a whole would have been far less assailable with a greater concentration and clarity of command. A decade later it is difficult to see what the real difference would have been had Anaconda been more successful, but many decisions certainly could have been made much better than they were.
References

Lambeth, Benjamin S. Air Power Against Terror: America's Conduct of Operation Enduring Freedom. Chapter Five. Santa Monica, Calif.: RAND, 2005.

Grossman, Elaine. Was Operation Anaconda ill-fated from the start? Inside the Pentagon. (July 29, 2004):http://di.net/grossman/army_analyst_blames.htm.