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.
Its not the cost, its the power usage. The 1080p LG G2 had incredible battery life, while the G3 (according to all the reviews) with 2K screen was a big step backward in battery life.
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.