This was pretty damn good Levi. You've got amazing ideas for creating not only a cool cinematic experience, but a really emotional one that draws on the right elements from the past to infuse nostalgia with a perfect balance of newness. I will agree with a lot of people here in saying that I wish 343 had understood the importance of balancing old and new so that the two can stand in contrast against each other. They could learn that from you.

Granted, I have no idea where the hell you're going with this, so every point I'm about to make may be completely off. But I felt the need, from one creative to another, to point out what I feel doesn't work in this. It helps my understanding of video games to pick these things apart from a conceptual level, and hopefully it'll help you with your future storytelling by understanding what doesn't work for certain members of your audience. :)

Firstly, I think there's an immediate problem in scope with the introduction (especially for the first level of a game), depending on the effect you were wanting to have. By starting out the game introducing us to the ships of the UNSC, the planet, and the larger view of space, you immediately set our expectations as the audience. Introductions are perhaps the most important part of a game, because they set your expectations for the rest of the experience. By showing us this larger world immediately, the UNSC fleet in orbit over a dusty planet, and then jumping down to that planet to reveal our player's situation, you've made us feel small, insignificant. Maybe that's what you wanted. Maybe that works for the Chief's new and unfamiliar situation. But in terms of player attention, this also has the potential to add frustration. To know that there's more going on outside of your area of influence. In the first Halo game and in Halo 4, this was use intentionally to overshadow your gameplay on the ships, to really let you know that everything you're doing over the course of the first level is really just the preamble to what the game is really about. In Halo 3, the focus is just on you as the player.

Here you come.
You've crashed.
People are worried about you.
You are revived and ready to explore your landing site.
Introduction to basic movement.
Your first introduction to a basic enemy engagement.

It's all a very gradual progression (in a positive or negative direction, depending on the story being told), and you don't really learn much about the larger conflict until the end of the level, when you're reunited with the main war effort (again, speaking about average players, not just fans). One could argue that Halo 2 breaks this mold by introducing the Arbiter and the Covenant's political tension before showing us the Chief, but that also sets the stage for the surprise we feel when we sympathetically jump into the shoes of the Arbiter. It was all building up to that one moment of payoff.
Again, you may have more planned later that will render this feedback obsolete, but I'm throwing it all on the table anyway. :)

I feel like you've got your camera jumping around like crazy. We go from two characters outside a ship to those same characters inside a ship (with no transition), then outside the ship again to show the space tether, then back inside the ship, only to have the characters walk out of the ship again. If feels a bit like the camera is jumping around as you think of stuff to show, rather than presenting that content in a streamlined fashion. It may just be the wording here, and I'm misinterpreting what you intended. That's the problem when trying to use text to explain something that should be visual in nature, so if I misunderstood something I apologize. But there's a lesson in that as well. Presentability always matters. I understand you're juggling a lot of important stuff, but consider posting up some diagrams/maps/really rough sketches. I think they'd help a lot, even if they're not super polished.

As an extension of this, the delivery of information to the player feels very un-paced to me. If you look at the beginning of Combat Evolved, Halo 3, Halo 4... the opening cutscenes are always very long and drawn out, giving the player time to get immersed in the sounds, sights, and atmosphere of the world before any information really starts to get delivered. Here it kind of feels like a lot of information is being dumped on the player at once, and certainly if they're new to Halo's fiction they'll definitely get it (you've set it up to be pretty clear from a symbolic standpoint as well), but regardless once the character starts explaining things I'd be afraid that too much exposition would ruin the mood for a lot of people. Basically, just slow it down a lot, space out the delivery of information a bit more so that each new piece can be that much more hard hitting. Half of what you've got here feels perfectly delivered, and the other half needs a little more juxtaposition.

The Halo seems to come out of nowhere. Given that you've said this is a follow-up to Shield and Sword for Halo 4, as well as 343i's Halo 4, I'm not entirely following how this is supposed to make sense to the player. Sure, Halos exist, they're dangerous, they pop up all over the place in the games... we get all that. But regardless, there was no build up to its reveal. It really feels like it comes out of nowhere.
Without any context (perhaps an earlier portion of the cutscene showing us what happened to the Halo so that we have more understanding when it appears) it just shows up and yells out "call to action!". There's little build up to why Chief has to return from his "retirement". It communicates something to the player along the lines of "Chief isn't fighting? No, this is a Halo game. Here's the Halo. See now he has to fight again." It just felt forced. The same goes for the fleet of ships in orbit. You're essentially telling two stories at once, rather than the single story you should be starting out with: the story of the player. That could sum up a lot of the issues I see here. It needs to focus less on the world and more on the player. Find that happy median. :)

The same goes for the introduction of the Flood. While I like how you're utilizing new forms here to explain that there's a larger story going on, it still feels strange to introduce something other than your primary enemy in the level which contains the bulk of your tutorial (unless the Flood are going to be the primary enemy in this game?) Because it's the first combat the players will experience, it sets their expectations for the rest of the game. Remember the reason the Flood feel so intimidating in Combat Evolved and Halo 3 is because they are unexpected and you always feel unprepared for them based on your past experience with that game. Introducing them right of the bat tells the player "here's what you can expect from combat". Also attempting to introduce a horror atmosphere before the player has had enough time to get immersed in the world means that all it has the potential to do is pull them out of the experience. If they aren't allowed enough time to soak things in before it all starts to fall apart in a terrifying way, the fact that the game is telling them they're supposed to be scared when they're not will only highlight that fact, making them more aware of the disconnect between their feelings and the feelings you want them to have.

It kind of feels like the Flood's introduction in Halo 2. The Arbiter level could more or less be considered a tutorial level for gameplay as an Elite. Because of how seamlessly the two gas mine levels blend together, they technically function as one playable experience in the player's mind. Just like Halo 2, you're essentially introducing the Flood while they're still trying to figure out where they fit into this new world, rather than after they feel confident. The Flood are best used as a method of humbling the player after they've built up enough confidence in previous levels. It's an effective formula that works to toy with the player's emotions when used correctly.

I guess mostly it just feels like a lot of this first level is tailored to experienced Halo players, rather than newcomers. Even if you're familiar with the controls and feel confident playing as a Spartan, the added buffer time between small and larger engagements can only help to immerse old players into the world more, and it's doing a huge service to those unfamiliar with the game as well. Think about an inexperienced player who's never used a shotgun against the Flood before. Hell, maybe they don't even grasp the basic function of a shotgun in combat (especially in a video game). They may get extremely frustrated right off the bat because you've handed them a weapon that, to them, just doesn't seem effective even though they're shooting in the direction of the "bad guys". Slowing things down for the first level can really only help everyone out.

I want to hear more about the "hodgepodge form". You might be treading dangerously close to Dead Space territory. It's important to get creative with new enemies, especially the Flood, but it's also important to keep in mind what makes them unique. Start getting too creative and adding too many forms and suddenly they'll become the Necromorphs or the Zerg.

I love the dialogue. I got a good sense of who this smoking character was, really got a feel for him through the dialogue alone, and you worked all the important information in without betraying that character. So excellent job with the writing there. :) The same goes for Chief's first line. While I think it's safe to have him talking a bit more now (as long as you are careful and don't overdo it), having his first spoken line be a triumphant return of sorts is very fitting for the character. I would just be sure that characters react to his silence realistically, rather than shrugging it off as normal.

I really like the way you're not just throwing characters right back into the fight, but taking your time with the introduction of who the character of the Chief is, so that as the player is going through all these gameplay motions, finding armor, essentially upgrading their gameplay and armaments, they're also symbolically reconstructing who the Chief is. They'll realize, at least on a subconscious level, that this building up process implies that John has been out of action for a while. He's not able to just leap right back in to combat, and this metaphorical rebuilding of his character and mythos (starting out as a "big guy" who's "looking for work" and transitioning back to just "Him? He's here?" That's an excellent buildup, perfectly executed as far as I'm concerned. In fact, it reminds me quite a bit of Dune Messiah. The prophet/protagonist has left the story, gone on a pilgrimage "to the desert". Having Chief start out in a desert is so fitting in this context and even in provoking more of Halo's religious imagery and atmosphere. I just love it. Symbolism always gets me excited from a storytelling standpoint, and whether intentional or not, this works really well.

Flood vehicles are awesome. Immediately makes me think of the "brain form" from inside the Pelican in Halo 2 that I always fantasized about seeing more of. It's got a lot of cool artistic and gameplay potential. Hopefully we can see some sketches for it someday. :)

Anyways, I was just typing as thoughts came to me. I'm sure I'm very wrong on multiple points that I didn't think through all the way. Feel free to point those out to me. :) Regardless, I think this is a cool idea and I'm excited to see where it goes, and I'm excited to dig through the experience from a design perspective so everyone involved can learn more about crafting these kind of stories. As 343 continues to push the universe in directions that many fans are unhappy with (although I like it), I think it's even more important that everyone is able to really get into game design and story crafting so that we can intelligently explain why we didn't like things and what can make them better. Halo fans and Halo developers can all learn from this process. :)

I guess the tl;dr version is: It's amazing, visually and symbolically perfect, but the gameplay and exposition just feels like too much, too soon. Don't be afraid to pace things out even more and really focus on easing the player into the swing of things. The heavy story payoff can come later for hardcore fans. :)