The early prototypes really nailed the core gameplay loop. The biggest changes since then have been to smooth out the complexity of the various subsystems, vastly increase performance so that you can have a vastly larger factory, and to introduce new types of puzzles such as the nuclear reactors. Blueprints were added fairly early on, followed by straight-up copy and paste a few years later, and they really changed the game. In the earliest prototypes, doubling the speed of your research required manually placing down all the belts and assemblers in order to double the size of your factory. With blueprints doubling the size of your factory is a much higher-level puzzle of cloning the pieces and plumbing them together, rather than the lower-level grind of placing a thousand machines. Trains were added at some point as well, which gives you a long-range transport capability. The circuit network was added so that your factory can make automated decisions without your direct involvement. And the UI has been greatly improved as well.