The actual terminology Moriyasu used is "free-to-start," meaning you won't have to pay anything to get started with either game, but they will of course be monetized. Given Nintendo's efforts in the handheld realm and the increasing number of mobile apps arising from the partnership between Nintendo and mobile company DeNA, this could very well be the norm going forward.
Unfortunately no additional details were given surrounding how the apps will utilize the free-to-play model. Animal Crossing on its own uses "bells" as a currency for players to purchase items, pay off their in-game homes and more, so it's very possible there could be a similar model in the mobile app. Fire Emblem is a strategy role-playing game notorious for featuring game modes where members of your party can succumb to permadeath, but perhaps a freemium model could offer options to bring them back for a fee.
This is an unsurprising move given the company's recent track record of releasing games like Pokemon Shuffle and Pokemon Rumble World as freemium options, both available via 3DS/2DS and mobile titles. Both rely on "energy" to continue playing if you run out of the allotted currency. Games like Nintendo Badge Arcade offer free plays each day and dangle additional badges to collect in the faces of those unwilling to pay further to explore, and Rusty's Real Deal Baseball gives players the option to haggle to purchase in-game minigames.
It's not clear how Nintendo will handle these high-profile franchises just yet, but free-to-play will almost certainly get more consumers invested than premium pricing. We'll have to wait and see what happens.