The FSF is calling for input, so consider the following my "high priority wishlist": these are all things I wish I had nicer representations in free software, and the lack thereof is hindering user freedom in some urgent way.
Server deployability tools
Deployment needs to become easier if we expect people to have any amount of digital autonomy. Processes need to become generalized, abstracted. I have written some ideas on this. I am happy to talk to anyone interested in improving this space... :)
Obviously somewhat self-serving, though my very reason for working on federation tools is due to my belief that a lack of federation tooling leads to many problems. Those arguments already well understood by anyone reading this site, so I won't go into details.
Implementation of the Social WG standards would be a good direction to take. Making this implementation reusable would be helpful.
"Unity competitor" level game engine
I've also written before on why I believe that games matter to free software and free culture.
But I'll particularly emphasize here: 1) proprietary games are bringing DRM to otherwise free software operating systems via steam, 2) games are currently the world's most popular medium, so if expression here is particularly hard, this is not good and 3) games are a great way to recruit new hackers, as this is the dream of many.
Assuming you buy those arguments, we are missing out on many opportunities of expression by the sheer amount of work required to get the basics of most games running. In the proprietary world, there is a game engine called Unity that seems popular not just for developers but also for artists. What is free software's answer?
Though it will surely come up, I'm not confident in the Blender Game Engine. Godot looks promising.
(As a side note, both of the following systems are fairly low-level at the moment and thus do not fulfill the above "full featured and easy to use", but some interesting things are happening in the lands of both Sly and m.grl (both by friends of mine)... I hope more happens with these.)
Password management tooling
Managing passwords is hard but important, and the current state of affairs in free software is a sorry one. Many users are turning to "LastPass", which astounds me in a post-Snowden, post-Lavabit world. How to provide a way to store passwords safely and easy to use way?
KeePassX and others which require manually copying around passwords I think are simply not usable enough given the massive volume of times users need to enter passwords.
I currently use assword, as "assword gui", when bound to a key in your window manager, gives a simple-ish prompt, with passwords dumped into whatever textbox previously had focus in X11. It also pleasantly stores passwords in a simple format: gpg encrypted json. Not bad, but there's no nice "management" interface, and there's no "mobile" (read: Android/Replicant) client.
It's great that we have GnuPG, but usage is hard. How to make easer? Maybe something like monkeysign could help web of trust things, but not only web of trust things are hard. SSL is also a great way to lose hair.
Relatedly, GPG could use your help, funding-wise! Consider making a donation.
Free phones and mobile devices
Is this software? Sort of, it also ties in with hardware.
Replicant is the best thing we have for phones. (I would love to see a resurrection of Maemo 5, but I realize I am in the minority here.)
Where is free software's competitor to Google Glass? Even if it isn't cool right now, some competitor will make pervasive computing popular. Do we really want to wait for the iEye before we start worrying that we don't have a solution? This, like free phones, requires both hardware and software.
Circuit printing pipeline
Libre hardware which can print circuits could possibly get us well on our way towards building hardware that's safe, reproducible, verifiable. It won't help with chips, still will require lots of soldering, but maybe it could help.
Easy, peer to peer filesharing between friends
The return of peer to peer? Yes indeed. I see this one is already on the list though. :)