I wonder if Apple are briar-patching a bit - since iPads are now using USB-C, and Macs are all USB-C (so things like SD card readers, wired earphones, HDMI adapters could work across the whole range) it would make sense if they bought iPhone into the fold... Yeah, the lightning connector may be slightly better mechanically than USB-C, but its a lot better than the older options. However, it will break iPhone users's existing kit, so it would be great to be able to blame it on the EU...
On the other hand, the EU seems a bit obsessive about this - we've gone from 30 different chargers with proprietary captive cables to, basically, two general types of socketed chargers (USB-C and USB-A) and 4 cables (USB-A/USB-C to MicroUSB/Lightning) which sounds like success. Seems like the next step should be to roll it out to other gadgets, not engage in a War on Apple.
On the other other hand, if the directive is properly drafted, adopting USB-C could be part and parcel of adopting things like the USB-C power delivery spec and the various alt modes - so there's no nonsense like "yes, our phone will work with a standard charger, but only in low power mode" or "yes, we've got a USB-C connector, but you still need to buy our proprietary dongles...".
I mean, USB-C is a world of hurt, but its a standard world of hurt which is often the price of standards.