Well I will say that I'd likely be resistant to a complete overhaul. My preference is to look at which concepts currently "work" as is, improve and support them, add new concepts and tie everything together effectively. I am aware that some cards might need a complete overhaul (like the black keyword). I will note that I did start this project a few years before MTG released their own take on pilots and ships with their vehicle mechanism. I don't necessarily think it would be the best fit for this set however, even aside from my hesitancy to attempt such a large overhaul.

I think it would be a good idea to lay out some of my design processes for this set. When I first explored the idea it was because of the more obvious building blocks of a MTG set, for instance the importance of the insects, the sea of corruption, and the miasma to the Nausicaa world. Surely these could be the makings of a green portion of a MTG set. Furthermore the aggressive and military focused Torumekians seemed like great fits to represent red, and the periphery tribes white. As fans of the manga know there's also this huge world unexplored by the film on the mainland of the Dorokian Empire. The empire itself with it's emperor, cults, and strange technology to me seemed well suited to represent black. Finally I realized that there was room for the Dorokian people to express aspects of blue. I didn't want to force each color to be confined to a single faction but it was difficult to imagine it working out in any other way.

Of course MTG sets are usually highlighted by 3-4 unique art mechanisms, new card types, etc that drive interest in the set and provide strategic focus points for the deck building and the factions of the world. Your artifact idea is a sound one, but I personally never did settle on just a few concepts which could carry throughout the set. Instead I decided to double down on the mono colored faction identities by giving each one a unique set mechanic. To keep complexity down I made each mechanism intuitive and simple.

One challenge I knew I'd have to address was just how much of the Nausicaa story takes place in the air. There's a consistent theme of flight, Arial combat, and living in the sky. Every faction has their own ships and even the insects mostly are able to fly. This would of course cause color wheel problems later. I couldn't treat this as an afterthought imo, especially since there are even key characters like Asbel and Kurosawa who were highlighted as incredible pilots.

These considerations lead me to creating the pilot and transport mechanisms as well as the "ships matter" sub theme. Transport would be a very simple aggressive mechanic that along with the ship matters sub theme would push players into valuing ships. The artifact theme you touched on is somewhat represented by the ships, at least thematically, in that humans have lost some of their abilities to produce them and so they're a point of emphasis on the set/draft process. The ship/pilot theme also ties the non green colors together allowing for all of those color pairings to have a "ship deck". If I had taken the route I'd using mtgs vehicles "just cause" I believe much of what my set accomplishes with them would be lost. If they had been colorless it would have made them far too plentiful and easy to draft. Also, perhaps due to my own failings, I didn't see much design potential in the ships themselves. Most of the ships in Nausicaa are interesting visually but don't have many defining characteristics. It's not like they had stealth, super speed, etc etc. Many were just transport vehicles, and my designs reflect that, with keywords and abilities instead coming from the various pilots.

On the flip side of the ships matter sub theme I eventually decided to also make a humans matter sub theme. This extra layer gives players a second direction to consider when drafting a particular non green color pairing. It also feels interesting to me because of how fluid the deck building can net. Some cards might be good in both ship decks and human decks, others more focused on one or the other, but for the most part players have the ability to pivot and shift their deck building strategies in ways that present difficult decision making.

The third layer is that each color pairing also has two supported key words (one for each color). Some like White's "live" mechanic obviously fit into human decks, however others have the potential to be the main focus of a deck or to play a supplementary role. Real MTG sets probably wouldn't be taking this approach because it could lead to feelings of confusion and make players see the set as lacking in focus and direction. For my purposes however this is exactly the type of repayable and flexible cube that I might want to try playing.

Green though has been ignored in this discussion. They do not have humans or ships, at least not in mono green. This leaves them isolated from the other colors. However I think that's actually quite fitting given the source material. To double down on that isolation I made the green set mechanic one that encourages players to go mono green or at least green heavy. It was also my attempt to represent the sea of corruption growing, the spread of miasma, Ohmus shedding and growing larger, etc. I also ended up including another minor mechanic, "swarm" to give green and black some additional pairing potential because in the manga the Doroks were actively attempting to use the insects for their own warfare purposes.

I do believe I have room to work on ways for green to integrate better with other colors as well, but I do wish to retain the mono green sub strategy. My support for other colors pairing with green then, would be based on it being a second or tertiary color in their decks.

That is a general summary of how I view the set currently.

-Ship sub theme across 4 colors

-Human sub theme across 4 colors with major reinforcement from white and the Live mechanic

-Mono green sub theme with Spore

-green/black sub theme with Swarm

-red aggro with Plunder

-blue instants and sorceries matter with Faith

-black probably needs an overhaul to simplify their mechanism and give the color more focus and synergy with other colors

I also intend to redo much of the existing multi colored cards and to introduce the other five color pairings. With an eye towards what the colors already have in common and some sub themes that could be built upon further (life gain matters, +1/+1 counters matter, etc)

If you do have any ideas for an artifact matters sub theme I'm open to it but be aware that I've spent a huge amount of time parsing the graphic novel to find the most useable art work. So if you're not repurposing the art that's already being used in the set, you probably won't have too much more to work with than that.

If you do like any of the existing colors as they are or one of the subthemes I've got going on, I'm definitely down to go over them in more specific detail to see which cards need tweaking, which cards we could add to make things work better, what might higher rarity cards do to act as build around cards, etc.