Kakashi's MS can be considered his trump card. A trump card is something that you think can deliver the final blow, it's basically your last ditch effort to kill your enemy or even a backup plan that can help change the tide of a battle when things are not in your favor and there is a possibility you can die. Kakashi knew he could handle all the villains in part one so there was no need for him to use MS and put his eyesight in jeopardy until part 2 when the Akatsuki began making their move. So why would Kakashi use his trump card or his back up plan if he knows he can handle the situation he is in. For example when Sasuke was fighting Itachi his trump card was Kirin. Why would Sasuke even think about using his trump card if he knows he can finish Itachi with a regular chidori.