I don't think the Lightning port will replace the headphone jack on the MBP, but in addition to it. Most likely in the space where the mag-safe is currently (assuming those case "leaks" are legit). This makes sense as people will be able to use the same cable to charge all their Apple products, while leaving all the USB-C ports free for data.
The SDXC card surprises me, and I'd like to know the reason for dropping it, beyond lack of space. Wireless doesn't really work for transferring files from SD cards, and adapters don't make sense for such a widely used standard. Even after everyone migrates their USB-A gear to USB-C there will still need to be an adapter for the SD card. Is there something on the horizon to replace it? USB-C out of cameras? Or wireless out of cameras?
But while I understand the convenience of maintaining a legacy USB-A port, it will actually be a useless port in a couple of years for many users. Keeping it around only encourages the continued use of legacy equipment, rather than upgrading as soon as possible. And frankly, only applies to things like thumb drives with built-in connection plugs. The reality is most USB-A devices connect with an "adapter" cable anyway, so a switch to a USB-C cable is easy and cheap. I can only imagine some cheap USB-A to USB-C adapters will come out for things like thumb drives which will add only a few mm to the size.