These are few things I thought are worth noting.

Typos I noticed:
when arriving into haven Kora says "You made it !", should be "You made it, !" (see the "," symbol I added?)
"will help get you acclimated with all that Haven has to offer." - word "acclimated" doesn't really fit into that sentence. I'm not English, so it may just be me, but that word definitely doesn't fit. Even "will help you get used to all that Haven has to offer" sounds... less out of place, though I'd think thrice and re-phrase it again if I were this game's developer. Too bad I'm not getting paid for this, instead I'm the one paying here ^^
Loving the irony: natives of this world are called 'strangers' :)
"Great, thanks for being a good ambassador!" - again, I'm not English but this doesn't sit well with me. Saying hello to natives makes me ambassador? I'd just remove this phrase.
"I need to get you up to speed on something called 'energy'" - "I need to inform you about..." sounds better to me. I'm not English, I prefer simpler phrases.
"alchemize weapons" - lulz, if I didn't know SK jargon I'd wonder what the hell that means - dropping your weapons into acid? I'd write "make" instead.
It would be nice if the game actually showed an arrow and pointed on energy symbol when Kora is speaking about it.

Bechamel teleportation is kind of confusing, we just leap straight to the next place instead of having our knight walk for us. But I've noticed no bad or hard to understand dialogs so no problems there.

When I walked out of training area, it said "press attack to revive"...

When I walked into "Defend Geo Knights" mission area (the very start of mission, small gate outside of force field), I saw a missing texture. Its on the left side of "low wall", behind a destructible block. Looks like small transparent side. Screenshot is saved on my PC, I can send it on first request.

Stuck at rank 3-2, can't progress to 4-1 to get me access to tier 2.

Generally I like how it looks, now the game feels more "completed". I don't like the idea behind "prestige" missions, though. And there definitely could be more dialogs.

Additional feedback, thoughts about improvement:
- How can we make this system more friendly and usable by YOU, the player?
Its too fast - make it longer. I did all missions to 3-2 in a few hours, and as soon as I finished all missions, I was "done" with my level and immediately reached next rank.
All missions are unique, thats nice. But they're too short and easy so you progress too fast. Make each rank last a day or more. Add few more missions, increase prestige limits so it takes some time to reach rank 3-2 where you get awesome items nearly free of charge. Or make 1* items do damage in between 0* items and 2* items, current 1* items do nearly same damage as 0* items. I did 13 damage with my hatchet, big beast slasher (or whatever its name), and 30-40 with calibur. The difference is just too big.
Some small animation upon reaching a new rank (bar filling up, star shining brightly ect) would be nice (same as heat accumulation on end of level). So that we get a feeling we accomplished something Big.
Lots of free gear is nice but a bad idea, IMO. Its too early, too easy to get, especially Calibur+Blaster. I say no free 2* gear to newbies, make them EARN it. Make it 5 separate missions to earn calibur, blaster, armor, helmet, shield. Throw bomb as a bonus to shield or helmet.
This won't make it more friendly, but will make me feel like working to get something instead of coming and getting free gifts everywhere. When I get everything free, I get bored and change game.
- Are there any parts of this system, or any specific missions, that are unclear or confusing?
There is no mission to check out how auction house works (price sorting, item searching ect), there is no mission explaining "this guy here can trade your tokens/sparks for awesome items", there is no mission stating "this guy here has all the standard equipment recipes, make sure you check him out. Or I missed it, and thus its easy to miss.
- Anything else that would improve the mission system?
A mission explaining general user interface would be most welcome. "This icon here is energy symbol, pressing it opens up energy depot", "this button here opens your inventory".
Again, less free items. Maybe recipes.
It would be most welcome to get a mission with reward being "3 UV roll ticket". Singe/double UV would do as well, as long as its a free UV roll. Bound to knight, obviously.

More simple missions just to extend the journey would not be bad. Instead of 2-3 missions it wouldn't be a bad idea to have 5-6. Just add few simple ones on top of existing ones. As always, first few rank progressions should be done with rank missions only, However, higher ranks should only be reach-able using rank missions and prestige missions and other missions.

"Deliver supplies" mission should not be a "press a button" mission, it should be a mission of actually grabbing the supplies and reaching depth 8 to deliver them. IMO, its more interesting than paying a small amount of crowns in Bazaar and pressing "submit" button. "Give minerals to chief geologist" should be about going to chief geologist instead of simple "submit" button. Same with other characters. And obviously there should be "assignment markers" like arrows pointing towards current objective or mission.

PS: scripted scenes, where you can't control your knight and something happens, are still missing entirely from the game. Ok, not entirely. There is a whole of 1 scripted scene in the game: when you open iron lockbox. For example: as you walk into the room (in some mission or not), some guy jumps out, throws a catchphrase or two at you and then you start fighting.