Though there is no direct connection to Ghost in the Shell is stated anywhere that I have found this anime would seem to have possibly been influenced by or even inspired by Ghost in the Shell. The theme is quite similar. As Chris said given that the time period would seem to be quite a bit earlier than the time of GitS the conclusion drawn by the OP that Motoko could have been part of this project wouldn't fit into the time frame. The nature of the alterations made to the girls and the purposes they are used for one could i suppose choose to see this series as a possible setup for the evenst of GitS. Basicly the common elements are that the characters involved are given life saving cybernetic augmentation and in return required to use these enhancements to do special ops work for the agency that provides the cybernetics.It seems that the implants in this series are imperfect which would lead one to believe that were the practice to continue and the implants improve to the point where even replacing an entire body woudl be possible while maintaining the practice of requiring service under the agency as payment for the cybernetics you would basicly have an agency similar to what we see in GitS.Of course this is all just speculation and possibly overly generous wish full thinking at that as there is no documented connection between the two series. Though there are enough things in common to at least merit some thought.   See 2 other replies