Hard to tell what Apple will do, really. EU legislation should theoretically force them to integrate a universal port (USB-C), but with companies the size of Apple, you never know whether they'll just ignore the legislation and pay whatever fine is associated with it. Depending on how much revenue they get from lightning accessory licensing, it might still be a net profit for them to just stick the proprietary lightning port.
They'll probably do something to the port soon, but whether it is merely updating the standard to support higher USB 3.X speeds, switching to USB-C or getting rid of it altogether remains to be seen. Your guess is as good as anyone's at this point.
I could see them switching to USB-C because I don't think Apple will develop a completely portless iPhone just yet. The inefficiency of wireless charging, slower data transfer speeds and possible issues with problem diagnosis all provide good reasons to stick with a wired connection for now. Granted, the Apple Watch is all wireless, but it's a different kind of device with a much smaller battery and no necessity for huge file transfers. But again, all just speculation.