I have a new hypothesis.
If the new laptops will utilize Siri / Touch ID / Apple Pay (all flagship Apple features that have been mysteriously missing from Macs), something that will require changes of both hardware and software, OS X 10.12 may be what we're really waiting for; it's the last missing piece. It may have been easier to build all of this into the next version of OS X, rather than do an El Cap update. Siri would certainly change the OS X experience heavily.
Think about iPhones; they launch parallel to the new iOS. You get two brand new products in one and get that harmony of the hardware supporting the software, and vice versa.
So why haven't we seen a refresh yet? Why no quad-core Broadwell? Because there's more to these laptops than we've been thinking. You can't release a 13" rMBP in March with Touch ID without a significant software change, right? If there is a new Touch ID / Siri / Apple Pay / Home button on these machines, it'd require a change to the unibody, hence the redesign. But, the function of this button will be deeply rooted in the OS, hence the need for OS X 10.12. You have all of these available improvements:
- New laptop design language (rMB): USB-C, color options, new keyboard, new battery tech
- Skylake processors, with new I/O options for TB3
- Introduction of Home Button features: Touch ID, Apple Pay, Siri
1 & 2 are ready to go. If 3 relies on a new OS X version, June makes sense.
This would make the wait more than worth it.