In short, studios who place their games at 80-100% off had a chance to reaching the "top-seller" charts, as the store ranks games by raw units sold. In other words, you could completely dominate the charts with abandonware by cycling games in and out for free. Why am I bringing all this up again? Well, you can't do that anymore!
According to game developer-centric newsletter GameDiscoverCo (which Destructoid has since gained access to), that practice is now dead: at least for "100% off" promotions. As the letter points out, other discounts still work, so you can still game the charts with other percentages. Like all things Nintendo, it's a start. It's baby steps toward a much bigger problem. GameDiscoverCo argues that a longer-term solution would be to change the charts to rank revenue in real-time, just like Steam.
As the newsletter notes, nothing was made public: that's how Nintendo rolls sometimes.