Different products are intended for different users. The new MacBook is aimed as a keyboarded equivalent of an iPad, right down to the choice of colors. It is intended to be used untethered and only connected for recharging when not in use. It makes no sense for desktop computers (like the mini) or powerful notebook computers that are likely to be connected to things.
Note that some people have been saying that this represents the demise of Thunderbolt, however Apple just revised the MacBook Airs with the faster Thunderbolt 2 (and I guess they did the same for the revised 13" MacBookPro), so it certainly doesn't look like Apple is heading down the single USB-C path for the entire product line. Keep in mind that the 2014 mini dropped FW800 (long dying) for a second Thunderbolt port and went to Thunderbolt 2 there as well.