I AM HERE! And I understand very little, but somehow that makes me more interested in this. :P As I said before, I am going to be absolutely useless in terms of making sure characters are in character, so I'll just skip over that part of the review...
I am excited to get to beta this though, because there aren't many mistakes and I can already tell I won't be smashing my head into my keyboard while looking over any chapters you send me. xD In terms of mistakes for this all I could really see were a few grammar, punctuation, mistakes and the like. Nothing too major or anything that would really take away from the story.
And... *drumroll* Anneliese doesn't strike me as a Mary-Sue! Hooray! I actually like her so far, and her interactions with the other characters were interesting to read. Along with her quirks, like naming and speaking to her weapons, (even if it was a reference to something else) she definitely has my interest. My only real complaint there is that I don't really have a basic idea of what she looks like, though maybe I just wasn't reading closely enough. *is tired*
I did find John intriguing as well, particularly at the end of his sort of POV where it said he was blind, I sort of figured it out halfway through, but I didn't know for sure until it actually said.
Speaking of his POV, it was very well written. You managed to paint quite a picture in my head there despite the POV being from someone who's blind. But you did great with descriptions all the way through the chapter and not just the beginning of it. Like I said earlier, I only caught a few mistakes here and there, your biggest problem seems to be with punctuation though.
At any rate, finish the next chapter already!

Well, since you've so kindly invited me to inspect your grammar, I suppose it would be terribly rude of me to refuse, no?

Anyways, you have a good concept for the descriptions you use to set the scene; however, your execution is a bit hit and miss. Like the first paragraph:

"The first light of dawn rose above the horizon in a fiery arc. Its blaze shone upon the Imperial capital, Zaphias; awaken its residents from their slumber."

First sentence? Good. Second one? Not so much because of the problematic grammar (not to mention it kills the mood). Also, you have problems with sticking to the same tense - again, here is an example from your first paragraph:

"The market was loud and oblivious to the elderly man entering the market square too absorbed in their own shopping to notice him laying down a worn blanket of burlap in his usual spot just outside the entrance to the lower quarter."

Starts out in past tense and then suddenly the reader is smacked in the face with present tense. (Same deal with the subsequent sentence, by the way.)

Anyways, this stuff happens a lot. If you aren't really confident in your proofreading skills, you should probably get a beta reader because these mistakes can be avoided really easily if you're careful. I understand if it appears in only one or two places but these are everywhere.

Lessee, there's also the problem with switching POVs; no, I don't have a problem with you bouncing from John to Annie since you have a section divider to denote that. What I'm talking about is this:

"Anneliese took a large bite of one, enjoying the flavor before pulling out two wooden lunch boxes."

Well, we started out in John's point of view but then, suddenly! We know that Annie's enjoying the flavour. John shouldn't know that stuff (and no, I'm not poking fun at his disability... although I will say something else about it later). Similarly, another example that really sticks out is how in the last section you suddenly go from Annie going ":D" at serving Alexei to... Alexei staring out the window and going "bah, pathetic bugs". This is very abrupt and shocking and it makes the reader wonder why we are suddenly privy to someone else's thoughts. So don't do it.

Aside from awkward wording in the narrative (pro tip: if it sounds weird when recited aloud, you should probably change it), some of the dialogue at the beginning sounds stilted. Like so:

"Well I suppose it's a good thing I'm not a bird and I don't fancy eating worms as my main food source." - Annie

"My main food source"? Who actually says that seriously in casual conversation? Now, it wouldn't look as out of place if that was a quirk of Annie's (that is to say, being oddly specific and mechanical about descriptions), but she's rather informal most of the time. Aside from that outlier, the dialogue sounds too... I don't know, rehearsed? Unnatural? Cliché? Perhaps all of the above. It just seems like I've heard those quips thousands of times before and there's no real twist to it that really personalizes it.

There are other miscellaneous things that I'm too lazy to give examples of but will mention anyways. You miss a lot of commas. Why is Lieutenant not capitalized despite being a military rank like Captain and Commandant? I don't think you really need that many footnotes (or at the least, the numbers that refer to them - especially that one that's basically only 'lololol Dragon Age 2 reference :DDDDD') because they're distracting. If you insist, at least try to see if you can make the numbers superscript.

Huzzah, the technical portion of the review is done. Now for my thoughts on your plot and characterization... or whatever I have to work with on the first chapter anyway.

Why is Flynn so chummy with Annie anyways? I mean, I know he's not a douche or anything but he's only that casual with Yuri, who he has known since childhood, so. He wasn't even shown being that friendly with the twins from The First Strike, and they were supposed to be in the same brigade. I can see Flynn being polite and friendly, but not so familiar as to tease her. How long has he even known her anyways? I think that this is a pretty big flaw since it honestly doesn't seem like you're doing much more than inserting Annie with a prewritten history but no substance (like character interaction prior to them being buddies - hell, it would actually be pretty interesting to see Annie try to befriend Super PMS Flynn a.k.a. FirstStrike!Flynn) to show for it. It looks lazy and will probably be facedesk-inducing if she meets up with other people who "recognize" her (*coughYuricough*).

I also don't recall Khroma being so sarcastic (or possessing a sense of humour), but I'll be more lenient with this considering we don't see too much of her. Still, I am skeptical. (On a semi-unrelated note, did the 360 version ever expand on why she was in the knights?)

I'll admit it's interesting to have an OC working for Alexei, although this part made me raise my eyebrows.

"Anneliese's Captain, Commandant Alexei"

Commandant and Captain are two different ranks and it doesn't make sense that he could be both. I mean, if you really wanted to make Annie subordinate to Alexei, why didn't you just make her a Captain? I honestly doubt a Lieutenant would report directly to the highest ranking officer unless there is something exceptional about him/her.

Small detail that bothered me about Cumore; John "accidentally" spilled water on him, right? Well, since Cumore is... Cumore, why didn't he arrest him for it? I can see the spazzing, but I can't Cumore not doing anything about it, considering how told his brigade to beat an unresisting Yuri for breaking into a house.

I'm confused about your timeline (which might be because you're using The First Strike in canon, because there are obviously no plot holes there, amirite?) because Flynn is apparently a "new recruit". Even though he served for a time in the Fedrock Brigade. Even though by the events at the start of the game, Flynn is a Lieutenant. (Seriously, it's the title he starts with.)

On your notes:

4: Dunno if you're referencing the cooking challenge where Flynn enters on your side or the 360 one. I'll assume the latter from context. I don't believe he's a terrible cook in the sense that he'll fail every dish. The PS3 version does have a skit where Karol says something along the lines of "you'll never know whether [the dish] will come out delicious or horrible" which basically enforces what Yuri said (I think. It's been awhile since I saw the 360 version) about Flynn - that it'll be good if he follows the recipe and bad if he doesn't. Maybe Flynn just likes to get creative with his cooking, idk.

5: I... don't get why you referenced that skit? Unless you just meant that Annie's opinion matched Yuri's? (On a side note, I honestly think that both of them were accurate in their descriptions - it's just a case of seeing the glass half-full or half-empty.)

Anyways, my vote goes to Patty. I mean, a token Tales loli with a depressing backstory? Seriously, what else do you need.

Shit this is long.

As soon as she said "Bianca's my baby and I would never leave her out of a fight" I got the Dragon Age 2 reference. Ahh, Varric was awesome D

I also like how you're including things from The First Strike, instead of keeping it strictly game-verse. Those little extra things help make a fanfic go further )

It's looking go so far, and I look forward to seeing more! It's so hard to find OC fics for Vesperia (