I think you're confusing what Cheesenium was implying. He was implying that the Heretics would be your allies in the future... Not the actual Geth. The brainwashing virus was only meant to affect Heretics, not the regular Geth.

But essentially, at the end of Legion's loyalty mission, there will be no more Heretics, as they will all either be destroyed (That being their main hub station) or turned into regular Geth.

Legion died when i ask him go into the hole in the final mission and i selected Samara as the second leader, i thought Asari with the age of thousand year, she have the experience to lead a small platoon to safely and wiping out the enemy with ease but Samara greatly disappoint me , i thought Samara would used her awesome biotic power she showed me when i first encounter her, but she is having a hard time dealing with the enemy, in the end Legion got a "lucky shot" from the collector when closing the door. * Sigh *

The second mission is the ask a person to save the survivor, i sent Thane because i like his cheesing "flash back" cut scene. I hope to see him in ME3.

The third is to choose biotic power, obviously i chose jack cause Samara disappoint me and secondary leader is Grunt, i thought Grunt is a good leader cause i find him brute force would take care everything, but then i heard the radio Grunt is having a hard time dealing with the enemy, then when closing the damn door, one lucky shot from collector and Grunt died. Not again!  and i thought to myself, with all the upgrade i gave u, u die in just 1 shot? Come on!

In hold the line, Mordin died which i think it is good, i disapprove his Genophage method, sigh i need him alive and i lazy to replay the game.

In the final boss fight, i kept Tali with me AT ALL TIME, because she is with me in ME1, and now ME2 she is still with me, thats loyalty to me, screw u Ashley. If Ashley were there in the final mission, i would appointed her as the secondary leader as she has the experience to deal with these situation.

Since i am full paragon,
I wanna ask if i play renegade, can i achieve "no one left behind"

Cerberus, if i help Cerberus in the final mission, he will used that data and set a bounty on shepherd head since he is no longer of used, either way paragon or renegate, Illusion man will come get Shepard but now have to deal with the reaper hmmm.