Quite simple really. Merely having a takedown process isn't enough to comply with the law. It must actually be complied with. YouTube went above and beyond in this, not only complying with DMCA requests, but not even requiring them. Megaupload's takedown process was a sham. Yes, they had a page where DMCA requests could be submitted, but actual compliance was poor, and intentionally so.
Compliance is a critical part of the DMCA. Once a site knows about infringing content, they lose safe harbor provisions.
Also, how do you think lobbying Congress would even hypothetically help YouTube in court? The DMCA doesn't have any different provisions for YouTube than it does for Megaupload.