The point here is that you have to create a new layout for the iPhone 5 (if you don't want your app letterboxed) and this adds an extra layer of complexity to the development. Seeing that there are also rumors about a different form factor iPad you would then have to maintain 6 different layouts (standard/retina/16:9 for iPhone, standard/retina/new layout iPad). Well or 12 if you have specific landscape layouts.
Designing UI on Android apps can be a pain since you don't have the "pixel perfect" paradigm, which is a common criticism on Android from iPhone developers, but if you manage to get them right you can get away with a single xml layout (of course, you can able to make things more complicated).
It seems to me that Apple are getting themselves in a bit of a mess with this. The tradeoffs with the "pixel perfect" method haven't really materialized until now.
Maybe I'm just being over pessimistic with this and it will be a non-issue, I really can't tell at this point, but I see this as the greatest issue with the iPhone 5 (which in turn is probably the reason they didn't increase the screen size earlier).