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I had the same approach as Gruber about a larger screen meaning more room for displaying more datas, and made same conclusions about the 4.7" model with same pixel density (1336x752 works fine). But while agreeing with the logic for the proposed resolution of the 5.5", I couldn't find the reason for another odd resolution like the one leaked and found in the last Xcode beta (736x414).

It's probably in fact simple:
The problem is still app compatibility and transitional support of old apps [before update with an adaptive (or at least, adapted) layout] with a scale up to fit the screen, eased with the choice to keep the same aspect ratio accross the different sizes (any other aspect ratio could have been used though, but then meaning letterboxed scaled apps).

Current 4" iPhones being @2x 568x320, there is a simple way to support a larger screen with a different resolution while both supporting scaling first and then a larger screen estate :
We have the relation 4*320 - 3*414 = 1280-1242 = 38 or 4*568 - 3*736 = 2272 - 2208 = 64
@4x rendering is probably not too costly (2x*2x compared to any non-integer random scale factor), and the display of an app at 2272x1280 (@4x 568x320) on a screen with a 2208x1242 resolution (then, with a small scale down after 4x, or even simply with a crop accounting for a marginal loss of data displayed) is probably not too hard on eyes given the high pixel density of a screen with at least a 5.18" diagonal (at 3*163 ppi maximum).
Basically, that's about the same magnifying effect as the display of the lowest resolution on a retina MacBook Pro 15" with @2x 1152x720 scaled up to a 2880x1800 display (iOS lacks sub-pixel rendering compared to OS X but it could be compensated by the higher pixel density).

And to continue with the analogy, the transitional scale up of 4" iPhone apps on the 4.7" screen could be seen as similar as the first lower resolution displayed on a rMBP15, @2x 1280x800 on a 2880x1800 display. And could also be considered that a 4.7" app with a proper layout would scale up on a 5.5" screen in about the same proportions (and with the rumors of a 2x 1152x720 12" new MacBook in the pipelines, the 12", 13.3" and 15.4" would be comparable to this new iPhone line-up).

So with both screen sizes, any 4" app should look quite fine simply scaled up to fit the screen, and with an adaptive/adapted layout both could offer a larger screen estate as logically often expected (and a bonus small magnifying lens effect on the 5.5" given the pixel density lower than 3*163 ppi). So yeah, if the 5.5" is real, 2208x1242 is a very good candidate to me too.
 
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