They could be moving from the number naming scheme of the naming rumours are true.
iPhone SE (4") small edition?
iPhone (4.7")
iPhone Pro (5.5")
However I don't think the SE will ever ship the same time as the iPhone and iPhone Pro. Just how it's playing out this year I think is Apple's plan moving forward. The SE will always ship in the spring and get the improvement of the flagship release six months prior (like how this years new SE phone is getting the 6s internals, minus 3D Touch)
- Spring 2016 = iPhone SE (with 6s power)
- Fall 2016 = iPhone and iPhone Pro ("iPhone 7" power and whatever new design and features)
- Spring 2017 = iPhone SE (with previous "iPhone 7" power)
- Fall 2017 = iPhone and iPhone Pro (whatever 7s power is and new features)
What I think this will do is, it gives Apple more constant high sales throughout the year and an extra peak sales time. Usually it's been September for launch sales, peak again in December for the holidays and then just kinda coasts along until next fall for the new launch. Doing it how I think Apple will set it up will have the same September for launch sales, peak again in December for the holidays and a new third peak in the Spring (March) for the SE launch. Which will keep overall iPhone sales high for longer.