Well, despite what you think landing the rocket was a breakthrough. Sure it involved the application of standard techniques in the industry but a combination so executed becomes more than the sum of its parts.

If you want something where SpaceX has blazed trail in science as well as engineering then there's thir work on CFL and more importantly supersonic retro propulsion. It turns out that the bow shock created by the engines is enough to serve as an ersatz heat shield and it protects the rocket when it would otherwise be destroyed during reentry. NASA's studying the data they've recorded for the purposes of applying it to Mars EDL. It's given them a chance to investigate an entirely new EDL technique which is important seeing as the Low-Density Supersonic Decelerator seems to be going nowhere.