In Sproggiwood, the story takes place around dives into the dungeons. Each dive is "rogue like" but the overall progression outside each dive is persistent.
I think this is the best way to do a random dungeon roguelike with a story.
That said, I wouldn't sell Sproggiwood on its story in particular, just the arrangement of everything. The game is fun because it's a good bite size style of roguelike for a phone with interesting/fun mechanics in play.