I don't think they left out anything intentionally. I think the SE is basically a trial balloon to see if there is a market for this kind of phone. As such, they reused the 5S case design and some components to save cost. The old display explains the lack of 3D Touch. The lack of MIMO for Wifi could be a result of the antenna configuration (perhaps also the missing LTE band). The Touch ID sensors could be left-over stock from the 5S/6. But overall, I think it's still a great little phone and almost exactly what I want.Not only is the next generation iPhone about 6 months away, but the SE already lacks things the 6 and 6S have. Don't get me wrong, I'm somewhat impressed with the new phone and what it offers, but I want a 7 with a smaller screen and I hate that you have to sacrifice.
If the SE is a success, we may see a 4" phone as part of their main lineup in the future (as well as the return of smaller Android phones).