I've been slowly working my way through the 3DS back catalogue. Right now I'm obsessed with Pokemon Picross. It's a nice low-stress game that will quite happily sit and wait for you to look down at your screen again, making it great for playing on the bus. :)
I have good memories playing Breath of the Wild on long bus journeys. As for retro games, any turn based RPGs are great because you can pretty much stop playing at any time. Pokémon, Chrono Trigger and the Persona games are among my favourites!
SMB3 also works really well with its short levels.