Citra 2021

Citra is a Nintendo 3DS emulator for PC that can run commercial games at 100% of their speed. Plus it can improve the games' graphics way past their humble Nintendo resolution.

The emulator can display both screens at the same time, though if you prefer you can set it to one screen at a time by assigning a button to alternate between screens. As far as the controls, you can use the keyboard or map the controls to an external gamepad. You can also use the touchscreen controls by setting the cursor directly on the point where you want to click.