This theory isn´t from mine but I wanted to share it with you.
Is possible that Lucci had direct orders related to Luffy from AoKiji and Garp?
When Luffy received the second Rokougan, Lucci could have killed him easily but instead of this he went to Usopp and he did the same thing before receiving the Jet Gattling.
Since AoKiji and Garp were the ones under the shadows of the entire Water 7 related sagas then we can conclude that they could have given to Lucci specific orders around Luffy and his crew:
-Capture Nico Robin
-Kill Strawhat crew with the exception of Monkey D. Luffy
I know that this a stupid idea but their miscalculation was that Lucci couldn´t be defeated and when Luffy won against Lucci the things changed scaring all the Navy.
This puts Lucci defeat to another scale in the entire events.