Citra is a Nintendo 3DS emulator for Mac that can run commercial games at 100% of their speed, in addition to adding a series of characteristics to improve their visuals above and beyond the modest resolution of Nintendo handheld consoles.
The emulator can display both screens in real time, though it's also possible to show only one in fullscreen and assign a button to alternate between the two. As far as the controls go, you can use either the keyboard or an external gamepad. In terms of the touch controls for the lower screen, you can use the mouse directly to click wherever you want.
Citra supports a ton of games from the Nintendo catalog in both 2D and 3D, though the emulator particularly shines with the 3D titles, allowing for a more intense resolution that completely transforms some games, making it seem like they're not even from a handheld device. Pokémon Sun and Moon and The Legend of Zelda: A Link Between Worlds, for example, look amazing.
Citra is possibly the best and most advanced Nintendo 3DS emulator you can find. It's an open source project created by volunteers that lets you enjoy your handheld games on a desktop computer.