Video games are a fickle thing to design, more difficult than designing an everyday object or coming up with a fitting cinematography. Not only must you know your audience, you must also anticipate whatever that audience might be doing in the game. Hence why a majority of games, especially those with a story to tell, opt to railroad the player, giving a set of corridors of levels that they have to go through in exact succession.
The other option, if you're making a game with a narrative, is try to be a Bethesda: make a huge, handcrafted, expensive world and populate it with quests that might or might not have anything to do with each other.
I've been playing Fallout New Vegas and it's hilarious how a lot of its things just don't match up with each other.
Or you can ditch the handcrafting entirely and let the computer randomize your levels for you.
(Bits removed from a game review. Thought I'll just dump it here instead of removing it entirely)
