EFF isn't getting it: powerful and rich people want this bill to pass for increased government surveillance, control, financial contracts, and bribes. It's probably that simple. They didn't make a mistake any more than they accidentally give the Pentagon or defence contractors ridiculous sums of money for useless stuff that just keeps people employed in their districts, their stock portfolios in the black, and their campaign funds full. This is part of systematic corruption. They just don't give a shit, they have incentives not to, and agencies promise them an exemption which they believe. (Wait, there's the mistake.)
Aside from huge voter push, the only thing that could change it would be similar money and power pushing in the opposite direction. Not talk, not lawyers, not faxes: one or more groups paying for and demanding curtailing of mass surveillance with ability to disrupt contracts, bills, or the politician's careers. Right now, only the pro-surveillance people are in that position. So, they're winning and will keep winning until people get how the system really works and make it work for them.