Emerald Aisle members have always been able to bypass the counter, so I'm not sure why that would be a reason for higher rates this year as opposed to the past.
Brand Positioning. Until the end of May, Alamo (previously targeted as a "tourist" brand) also allowed customers to bypass the counter. It was essentially the same thing as Emerald Club (minus the free upgrades).
Because of this, it was hard to position National as being worth more money, since the service was essentially the same either way, only difference being National was positioned towards Business Travel and Alamo towards Leisure Travel.
Enterprise has owned National/Alamo for a while and they're finally sorting out the different brands.
Now, they're positioning National not just as a business brand, but as a "premium" brand, with Enterprise as the "everyday" brand, and Alamo is now more like a stripped down "value" brand than a full service agency. Emerald Club is one of the reasons that ERAC can justify charging more for National over their other two brands. If you want a deal, Alamo's going to be the brand that has it.
National isn't going after the consumer market anymore. They're going after the big corporate contracts which may be with Hertz and
Avis, not
Budget, Dollar, Thrifty, Advantage, etc. Because it's now a 100% shared rental fleet at major airports, the company has no incentive to rent cars for less under the National brand, when they can rent the same car under either the Enterprise or Alamo brands for less without pulling the National brand downmarket. They want you to pay extra for Emerald Club and for Frequent Flyer Miles.