I just played this part of the game for the first time, and I had to kill Legion and the Geth. There was no way I was going to let the Quarians die. I wanted to broker peace between the Geth and the Quarians, but the Paragon option "Rally the fleet" was grayed out. I had everything set up right. In ME2, I completed Tali's loyalty mission without her being exiled, I destroyed the heretic Geth, I solved the Tali/Legion conflict peacefully and kept both their loyalty. I saved Admiral Xen in ME3, and I completed the mission "Priority: Rannoch," AND I've been Paragon ever since starting ME2.
I hate, hate, hate, hate, HATE that I had to kill Legion and the Geth.
The Paragon/Renegade system in this game is so unclear it's sickening. I've heard varied results on the internet. Some saying that they had full Paragon meters and never received the option to rally the fleet, others saying they didn't have full Paragon meters and DID receive the option to rally the fleet. I cannot comprehend why BioWare made this system so confusing and inconsistent.