Mar 21, 2016

3 reasons:
1.) market presence-- they aim to have a continuous flow of new products, which is also why they're announcing this now, and not in june when they will likely be announcing the i7
2.) pricing -- the SE is being sold, much like the 5C was, as a budget product. it's last year's hardware & 3 year's ago casing. and therefore, it's cheaper to produce, and can be sold at a cheaper price. they couldn't have done that a year ago when the internals were still fresh and more costly to produce.
3.) cannibalization -- if they would have released this at the same time as the 6S, then many people would have opted to stay with the screen size they already adored at the time. apple would have been forced to sell it for cheaper, and therefore, would have lost revenue even though they would have sold the same amount of devices as they did with the 6/6S launches.

...really, it comes down to money, with #2 actually working in favor of the consumer.