I know many of you would dislike my opinion, but:

I think Mako did him a favor. Yes, she's a horrible horrible bitch. No argument there. She was also really into Shirou and loved him, and wanted to try everything to keep him. But, since she loved him she also wanted him to be happy, so she thought of a plan: "I'll fake a pregnancy; if he loves me and wants to be with me he'll be happy and we could marry, if he gets distressed and depressed it's time to let him go". And she did just that. She tried her best to capture his heart, and when she couldn't she let it go. She could have not done this very harsh step of faking a pregnancy and they would have eventually gotten married even though he would have been unhappy. We all know he wouldn't have broken up with her on his own. We know for sure. But she chose to give it one last try, and then let it go. If she hadn't given him this fright of a pregnancy, he would never have been able to accept his true feelings for Masami. He thought it would always be a possibility, that Masami would always be there, but that's wrong. Both Mako and Masami were suffering because of him. All 3 characters had it rough, but Shirou was the passive one, the other two at least tried to change the situation. I'm so happy it ended the way it did. <3