I think it's actually pretty clever. Developers clearly have trouble writing apps to support arbitrary scale factors. Resolution independence was supposed to be a feature of Windows since Vista was codenamed "Longhorn" (before 2004), and Windows is still a mess on higher-DPI screens 10 years later. Making it so developers only have to think about 1x and 2x and 3x makes the task easier.

Also, look at it this way: with the diminishing returns of resolutions above 300 dpi, is it really a big deal that you won't get the absolute best use of the iPhone 6+'s 400 dpi? Seems like a pretty reasonable trade-off to use that extra resolution in a way that makes resolution-independence easier for developers.