Complete the series. Merge the citites.
Cascadia is big land. Why have to all things happen in Glass? Why don't send new Faith fight other things, to other cities, or better. Make whole new map that consists of all citites, where you can travel in. Make it social, massive, multiplayer. What about dedicated servers, where players can, beside main campaing in singleplayer play with other people, exploring map, add user made content. I think, if you would do some challenge for fans, like... "Make something for ME3 and we gave you early BETA access", that would help you a lot, cause I think, beside me, there is plenty of graphics, programmers and idea-makers that could help you out and gave you some impulse.
Let players make their choices and depend on them, let Faith's fate changed. Add some stuff beside fighting and running. Some logical levels, where you must think harder then thinking about "choosing" which path you should go. Let player do some hacking on its own. Put there "learn curve", where player has to remember what he did like hours ago, remember code line, to insert it somewhere else. For this purpose, add some "Diary of Faith".
Add some cool things, like... Where you can earn "style points" cause you add mechanic of doing tricks in the air, like jumping from certain height you can do backflip etc. Progress leveling-up and let it be inserted in more then just pure "learning abilities". That idea was and still is awesome, but it needs more uses and more ways to earn skill.