If you look at the world of business-targeted Windows 8 tablets, many of them have 128GB storage options...including the upcoming Surface Pro. The logic is clear, especially if you're in a business where you need to store tons of files locally and don't want to sync in the cloud. In that sense, a stepped-up storage option for the larger iPad makes obvious sense.
The real benefit of 128GB of storage, though, would be in the 11-inch MacBook Air. That $999 entry-level device is the only MacBook under $1000. It's a wonderful, compact laptop. It's fast. But 64GB of onboard storage just doesn't cut it...especially when you can't swap in a standard SSD upgrade.