I think this suffers a LOT from simply trying to recreate the original game in tabletop form, rather than trying to emulate the overall experience. There a lot of "Video gamey" features and mechanics that don't make sense when you aren't playing a free to play looter shooter (mod polarities, endo, health/energy orbs, affinity range, Duviri decrees, RIVEN MODS of all things, CRAFTING TIMES). You end up carrying over things that were already tedious or annoying in the original game, and are just unnecessary in pen and paper.
There's also a lot of math you have to do that was clearly never intended to be done by hand, since it involves items and modifiers copied directly from the game with few, if any, adjustments. For example, the rules for rolling to hit say "For ranged weapons you will roll a number of attacks equal to your fire rate", which would be a d100 roll for each shot. The Prisma Grakata, the fastest firing weapon in the game, has a firerate of twenty-two without any outside modifiers. Unless i'm missing something incredibly important, thats 22d100 in a single turn. At minimum, because each shot that hit would also get more rolls to see if it becomes a critical hit, and if it inflicts a status condition. For a fast paced game about space ninjas, having to stop to resolve dozens of dice rolls before seeing if something even gets hit, let alone how much damage they take, seems rather unfitting.
I think you need to take a step back and think about what you want in a Warframe rpg, because as it stands, this really isn't suited to telling stories in the warframe universe, it's suited to simulating the things a warframe player deals with in game - including calculating all the scaling and modifiers that the computer is supposed to take care of.
As negative as i've been, i don't want to just say your entire system is bad and leave it at that, so ill point out some things i think you did well, and some i can provide actual suggestions on instead of just complaining:
- I think the d100 was the best choice for the basic resolution system, as much as i complained about it when there were dozens of them to be made. I think the "roll under" approach you took with rolling for crits and status effects is best, and could work well for the basic Skill Rolls and rolls to hit, if the latter used an "accuracy" stat for weapons. Maybe other dice mechanics would be better for say, seeing if a bunch of projectiles hit their target, but i think the one you picked for general purposes was well selected.
- Placing the five focus schools as the equivalent of character classes while the frames themselves are mainly just equipment was a great idea, as was only making the player rank up their focus abilities while the warframes are already at max rank. (while we're talking about the tenno, you may want to check the description for Void Sling again, i don't think thats what you meant to put there).
-Putting the weapons and mods into their own docments was smart, but i feel like some of the more advanced options could follow suit. Things that players aren't going to have easy access to until later in the game, like arcanes, necramechs, helminth, rivens (if they have to exist), etc. You could easily break up the "core" rulebook into "basic" and "advanced" books. You could also put the narmer/murmur/sentient factions in the advanced book, given they dont show up until later on in the original game's story.
-The layout of the whole thing is just beautiful, especially the art at the top of the planet descriptions. I know its all just official art or screenshots, but you know where to put it.
I'm excited to see where you take this project, even if i didn't seem to have much positive to say about it. Warframe is my favorite video game, and being able to play it in table top form would be amazing. Whether you want to focus on the tactical side with the various mods and weapons, focus on the lore and storytelling aspects of the game, or just replicate the feeling of space ninjas doing the space ninja things, i think it can be a great game. I just don't think you're going to achieve ANY of that by replicating game mechanics 1:1 using dice.