Re: This movies connections to Nick Fury vs. S.H.I.E.L.D. (potential SPOILERS)
There seems to be an ideological clash between Fury's line "SHIELD takes the world as it is, not as we like it to be." vs. Pierce's "To build a better world, sometimes means tearing the old one down." Fury is concerned with "neutralizing threats", while Pierce is "building" and "shaping". The later sentiment matches the apparent militarization of SHIELD.
And I definitely agree "shaped the century/do it one more time" is towards WS. As he is finishing the line, you see WS grabbing a gun, and shooting the exploding disk-thing at Fury.