As I understand it, the EPA does an independent, third-party estimate of each car's mileage. If there is a major, consistent discrepancy between EPA estimates and actual end-user experience, then the problem lies in the differences between testing and real-world scenarios. While there is probably no conspiracy on the fuelly website, I think it is equally unlikely that there is a conspiracy with the EPA's testing.
More than likely, Hondas respond poorly to the EPAs testing but better in the hands of average drivers, while Hyundais do well in the EPA's testing but poorly in the hands of real drivers.
I'd also be curious to see the demographic breakdown of the people who are reporting. It's very possible that people who bought Hyundais instead of Hondas saved enough money in the initial purchase that they aren't as concerned with getting great mileage/paying less for gas. It's also possible that older people are more likely to be able to afford the "better brand," and as a result you have older (and consequently more subdued) drivers in the Hondas.
But in the end, there are just too many factors to take into account. Let the EPA do their jobs, and if they've gotten it wrong, they should check the reasons why. This isn't the same as GM advertising the Cruze at 45 mpg before the EPA even had a chance to rate it.
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