As a relative outsider looking in I wanted to add my two cents. Coming from a free software standpoint and having delved into Ubuntu Touch recently http://nicorikken.eu/blog/ubuntu-calling-for-freedom/ after having looked into the benefits of open hardware designs for mobile platforms (also on my blog) I have now also looked at the option of Sailfish OS. As I have an old Samsung Galaxy S Advance which is perfectly fine hardwarewise but now stuck at Android 2.2 I understand the practical issues of lacking firmware updates all too well.
It seems to me that the goal of the Fairphone OS should be to suit the use cases of a wide variety of users (including non-technical) throughout the lifetime of the hardware, starting in the present. Unfortunately these sub-goals are in conflict with each other. To extend the lifetime of an OS, full control would be ideal, making the case for an open source software stack. To suit the variety of use-cases a wide selection of apps is needed of which newer versions should be supported, making the case for a recent Android version with the important addition of the Google Play Store to allow for vendor-specific apps which aren't available in say the F-Droid repository. Not seeming to be OS-related is the fact that performant hardware (in the largest possible definition) is needed to again suit the use cases of users in the present and to extend the phone's value into the future.
To obtain performant hardware Fairphone is likely to only have a limited set of options to consider, as was the case regarding the FP1 when a base model was selected from a catalogue. The unfortunate reality is that most chips nowadays require drivers in binary format, only available under a non-disclosure agreement and only for Android. Luckily Ubuntu Touch and Sailfish OS (by Jolla) support Android hardware by running a minimal Android version with the drivers (Sailfish as well?) and communication to the drivers using libhybris. This frees the rest of the OS from the ties with the underlying hardware. Ubuntu toch for instance intends to keep all their upcoming phones up to date by abstracting the driver part, whilst updating the upper layers for all types of phones they support. Sailfish OS could be used in a similar way. What differs Sailfish OS and Ubuntu Touch other than their interfaces is the fact that Sailfish OS is able to run Android applications using Alien Dalvik, thus giving access to many core apps (e.g. for email and chat) and vendor-specific apps (e.g. for banking and social networks). However this holds a big IF, as this software is to be licensed from Myriad which might not be willing to support phones outside of the Jolla brand http://forum.xda-developers.com/jolla-sailfish/general/alien-dalvik-licensing-issue-t2694127
Assuming Fairphone is able to negotiate any requirements for the hardware or the board support package including the drivers, there is a real potential for building software on the phone which can be kept up-to-date with other developments. Using Sailfish OS with Alien Dalvik seems to tick the boxes, but as this support for Android apps is no guarantee, Ubuntu Touch is still a relevant option or even a more matured version of Firefox OS or Tizen. In that regard a hybrid approach would be possible where users would be able to start off using Android (or another OS if app availability isn't such a problem) and move to another OS later when more applications have become available.
There are still a lot of questions to be answered, but the question whether or not Alien Dalvik would be available to Fairphone would have the greatest impact on what other options to consider, and thus will need to be answered soon.