Well, for one, he'd have been defeated by Kakashi and if not captured by Jiraiya for sure, which would have ompletly derailed that whole thing. He wouldn't have been able to re-mindrape Sasuke, which would have removed one of the factoors that influenced Sasuke to defect to Orochimaru.

If Miraculously the entire manga continued on schedule despite Itachi's lack of Mangekyo, without Susanoo he would have been killed by Orochimaru, who'd have then jacked Sasuke's body and gained Indra's Demigod Chakra. If by some miracle that didn't happen, without Mangekyo Sasuke could't transplant Itachi's eyes into his head, meaning No eternal Mangekyo, meaning Sasuke would have been blind from the Hokage Summit on, and, um, without Eternal Mangekyo Sasuke's left eye wouldn't have become a Rinnegan when he recived the Sage's chakra, so he and Naruto would't have been able to undo the Infinite Moonthingy, assuming Sasuke's tusanoo would have been stong enough without Eternal Mangekyo of Rinnegan to stop them from bein trapped in it or that they could have defeated Kaguya without the major power boost that Eternal Mangekyo and Rinnegan give to Sasuke.

Basically, dropping Mangekyo from Itachi fracks up the entire storyline.