First, quite a lot of indie games build an engine and then numerous variations of levels to support a plot. Braid, Bastion, Iji, Super Meat Boy, Gish, World of Goo, and many more where those came from follow that model: impressive engine, pile of well-designed levels, plot. In those cases, the ability to create more levels and add some technical variations can nicely extend the lifespan of a game.

Second, and even more importantly, the much broader space of design ideas in indie games means many more interesting components with unusual variations. Braid has a physics engine that supports time-based mechanics. Super Meat Boy has an extremely impressive record-and-replay mechanism (used to great effect at the end of each level to show you all the ways you died simultaneously). Several indie games have very impressive lighting models. The Bit Trip games have music syncing engines. Many indie games have impressive dynamic-content-generation engines. The more of these components that become readily available, the more impressive the starting point for any future indie game.