I wouldn't necessarily describe them as tool boxes myself, I just think there's more then one aspect of gaming, and that sometimes you can be relaxed on the story aspect, if you have something else (such as building, or exploration) to take its place. By focusing on those mechanics you can leave the story to a quick intro, and outro, with other more ambiguous bits sprinkled around the game, all while leaving how they fit together up to the player. Don't starve is a good example of that.
As for games getting boring in the middle, there are tons of ways to improve that, from simply giving the play a new and interesting way of shooting the enemies, to a setting change. I think the game that is best at offering ways of keeping it fresh would be fallout 4. If you're getting bored of the main plot, there are hundreds of side quest available, all with their own story arcs. Getting tired of the same part of Boston, pick a direction and go exploring. Wish there was a giant, cyber-punk-esqu, leveled city in the middle of the wasteland, build it. Just want to shoot waves of bad guys, walk for a minute in any direction. That is a game that knows how to keep it fresh.