Not sure about what to say, since I'm a lot more focused on seeking and reporting bugs that in gameplay quality, but I have some suggestions to make (just in case it could be possible to be reliable):
Alice: She has a big scar around her neck, like Jed Cooper ('Hang 'Em High') or The Kurgan ('Highlander'). I was wondering if her voice had to sound hoarse, rough and/or raspy (in other words: noticing that her larynx and trachea were badly damaged from the day she gained that scar, and now she has issues to speak correctly).
'A breath of hope': the pilot says oftenly: 'If it helps, the should be an Aleph portal around there in the shape of a monolith'. At first, I thought he was saying there was a souce of Aleph in the shape of a monolith around the scene, to charge the character with an Aleph and then discharge him on each monoliths, but then I realized that the pilot was referring to the whole set of portals that must be overriden; since you see the portals on the cinematic (and thus, they've catched the player's attention since they are stranglely shaped and crimson/golden coloured) I think it's not necessary for the pilot to say the phrase, or at least not so frequently.
Current narrative issues: Since this game focuses on being an asymetrical adventure game, with a strong narrative as one of their crucial and killing features, maybe it's not too early to start speaking of them:
Lycus: You can select Lycus for the mission where you have to rescue... Lycus!!!. Did I missed something related to clones, or so?.
Shae: Same with Shae after rescuing Lycus.
Hans: At the cinematic before the mission to rescue Lycus Hans says to Harec that, after that mission, he'll be away for a while since his bussiness can't wait for longer. 'Whatever. Let's go!' responds Harec. But then you can select him at the following mission, the one regarding to rescue Shae. I understand, at least, that if Hans said this, he'll be very busy and won't be available for ...who knows?. Three or four missions?. Maybe even al this time he wasn't available could be launched as independent, spin-off missions.
May it helps in some way to make a better game.