I might be reading too much into thing but I honestly feel Kai Leng was intended to be Shepard's foil. The very first time hes get introduced in the game you see him standing behind the Illusive Man talking about how he has his own solution to the problem. Kai Leng went through a process to rebuild his body like Shepard and is given the same objectives as him on the Citadel, reach the council, and on Thessia, get the beacon. It also get implied via the video logs at the Cerberus base that he has some kind of jealousy towards Shepard when TIM says he still respect Shepard and responding he is better then him.
I think it would have been neat if you got the chance to square off against Kai Leng on all the main missions and he had his own squad and crew. Eva Core could have been their EDI and I'm sure the comics and books have other named operatives the could have used. They have the plans for the Normandy for the SR-2 so they could have had a modified version of it. It would have made an interesting and Cerberus' constant meddling would have had a face.

I can't let you do that, Shepard