>Cobbling parts
It's pre-built. You plug in power and an SD card. Maybe throw it in a case if you're feeling fancy.
>Getting viruses from torrents
There's so many reputable sites for roms now this hasn't been an issue for like a decade.
>Aftermarket controllers
The Pi setup supports Xbox, PS3/4, Wii bluetooth, or hell, just get a USB adapter for the original NES/SNES controller. All out of the box supported. Bonus points: the controller cable isn't like, 2 inches long like it is on the NES Classic.
>Finding the best emulator
RetroPie already did this for you. Out of the box they're all configured and ready to go. The only things that are still fiddly are systems like PS1 or some really garbage N64 games, as they still aren't emulated perfectly. Anything older is amazingly good and honestly better than even the NES Classic.
All you do is toss the roms in the right folder and you're good to go. If you want to get fancy, you give it internet access and let it index them too for artwork, etc. It runs a UI designed for controllers on a TV and is easy enough to use that even my nephew can handle it.