Konami had to Sell an App to get around this problem. The games in question "Love Plus Series" lets you continue your relation ship with your girls. It's a Japanese only. (It's rated CERO C. Approx ESRB T or PEGI 16. )
Actually Konami actually wanted to give the app away for free, but they couldn't. It's priced at 200Yen which is the lowest a 3DS eshop item is. http://www.nintendoworldreport.com/news/27448
So GameFreak could be forced to make you to buy their app too.