There is also the question of ABI - as long as you want to make it possible for people to submit closed source compiled applications to the Jolla Store that's something to think about. In Fedora, everything just gets rebuild and fixed as necessary due to all software being open source. But that should be something Flatpak should be able to solve as it provides stable application runtimes independent of the distribution underneath. (...) Actually, I would say the main issue is Sailfish OS not shipping Qt Quick Controls while Nemo had Controls from the start and based their own QML component set on them. If Controls were available on both platforms, application authors could opt for having less native look but supporting both platforms (+ desktop Linux/Android & Windows). Actually while I can understand the attempt to "feel native" and do your own thing, in my opinion all the distribution specific QML components are causing more bad than good, due to destroying application compatibility and leading to even more fragmentation. It would be like if you could not run a GTK3 or Qt5 application for Fedora on Ubuntu due to Fedora having Fedora components and Ubuntu having Ubuntu components (well, Ubuntu kinda tried that with Ubuntu Touch components and how it went...). I would rather see any mobile usage shortcomings being fixed in Controls, with possible some platform specific theming of UI element. That seems much more worthwhile to me. As for potential solutions for the Sailfish OS/Nemo/other compatiblity issues:
opensource Silica so that it can run on Nemo and elsewhere provide Controls on Sailfish OS use Universal Components like modRana (makes it possible to have a single application UI code that works with both Silica and Controls) use Flatpak to decouple the application runtime from the distribution and have a runtime provide a component set
Another part is the support for Android applications and the necessity to use Android drivers on mobile devices. This quite effectively prevents being on the bleeding edge. Using some more or less niche hardware that has native driver support for Linux could be an alternative, however, it would severely limit already limited availability of devices to run Sailfish.