Garrus fought off half of Omegas criminal underworld (read: half of the stations population) by himself. Had a bit of help, and all the help died, but that's no less hostile than the omega 4 suicide mission. Wasn't a mere hit and run assault either, he actually stood his ground for a really long time.
Samara, is a biotic goddess honing the art for thousands of years.
Jack is just a natural born biotic prodigy honed by a rough a childhood raised by cerberus.
Liara is basically the Mass Effect equivalent of the NSA.
Joker is the best frigate pilot in the alliance
EDI is a self aware AI, able to do everything perfectly, and by the end of Mass Effect 3 even has some ability to think creatively
My take? Illusive man didn't need shepard at all.
Garrus is a good leader but I doubt he would work for TIM on his own and nobody in Cerberus is taking orders from a Alien.
Samara isn't a leader. Once again she's an alien
Jack working for TIM on her own is laughable, heck her working for him with Shepard is still laughable.
Liara was too busy playing Shadow Broker and oogling Shep's dead body armor, and she's an alien
Joker only flies
EDI was just a part of the ship
So...who was gonna lead these people or get them to join?
Besides, Shepard is the PC, that's what makes him special unless you want to play canon fodder #5.
Besides, even if ME2 gave us a different PC. I doubt Garrus, Liara, Joker, Tali, and Dr. Chakwas would join. I would probably throw Legion in as well considering that he's familiar with Shepard and not some random PC who works for Cerberus.