Apple has pulled off quite the accomplishment. No longer needing to innovate, or create high performance devices, they now exist effortlessly by simply remembering to affix the magic Apple Logo. At the zenith of the companies history, they're now free to do as much or little as they wish without consequences of any significance. A very unique operation indeed.
I say no. If they came out with all of these phones at the same time, they'd not make as much money. $399 is a steal for what is, essentially, an iPhone 6s. If people go for the SE, they are really only deciding based on screen size and price - and price wins out most times.
By stratifying their products they will sell more. You can wait for the 7 series or wait even longer for the next SE series. This is marketing genius for the company. Either way, they get yr $$.