That should just be a trivial annoyance, because Apple sells a $30 adapter for plugging old-style peripherals into the Lightning port. But that adapter won't work well with card sleds, so if you're deploying iPads to associates for in-store mobile POS, you'll either need to upgrade all iPads or start using two types of card sleds. (We calculate that PCI-friendly sleds with Lightning connectors should be available about 12 milliseconds after the even-newer iPad starts to ship in November.)
And that's the type of thing that drives central IT support crazy, because it means twice as many spares to keep track of—and the sled that just broke is always the one you just ran out of. Even if they're both available, mistakes happen—and when central support overnights the wrong sled to a store (or a store asks for the wrong type), both the sled and the iPad are useless for POS until the right sled arrives.
This is exactly why IT support groups hate having two incompatible versions of anything. It's not a show-stopper, just a really annoying source of complexity. And no matter how loudly they grumble, support people can never get IT upper management to see why it's a problem.
There are workarounds: Aside from replacing everything with new versions (no doubt that is Apple's preferred fix), iPad-using chains could stick with old-style sleds and start (or keep) buying iPad 2 tablets, which are still available and use the older connector. That means two (interchangeable) types of tablets but only one type of sled. The iPad 2 is also cheaper, but it has lower screen resolution than the new Retina iPads, which matters if associates are showing videos to customers.
Besides, that's a stopgap. You can't keep buying antiques forever.
Or a chain could move tablets around, so each store uses just one type of iPad and one type of sled, eventually cycling out the older machines entirely. A store could still end up being sent the wrong type of sled (or replacement tablet). But the rest of the time, each store would be dealing with interchangeable parts.
It's not a major crisis, just messy and inconvenient. In fairness to Apple, the company has been using that connector since 2003, and it was bound to change sometime. In fairness to your IT support group, they're right—any time is a bad time for a messy IT transition in your stores. Let the grumbling commence.