I've been thinking (over-analyzing) about the story in this game, and none of it makes any sense. I decided I may as well post some of my thoughts here, in case anyone else found them of interest.
1) We're stranded on a distant planet, and the only way to escape is to retrieve a mysterious, unknown power source hidden in the center of the planet so we can power the Skylark and leave cradle.
How do we even know there is a power source in the core? All knights who speak of it always start by saying things like "There seems to be..." or "We believe that...". Such words represent doubt and ignorance. Why are we trying so fervently to break into the core, if we aren't even 100% sure that whatever is inside will be of any use? If there is a power source, are we really 100% sure we will be able to use it to power the Skylark? If it really can be used to power the Skylark, are we sure that the Skylark will even fly again? Isn't there at least one undeniable truth for us to justify our efforts? If not, that means everything we've done so far is based purely on assumptions, guesswork, and wishful thinking.
Also, why do we need to fix the Skylark? Can't we use the large variety of resources that are available to us on Cradle to come up with a more practical solution? I'm assuming nobody in the Spiral Order has ever thought about building smaller craft and sending a convoy of knights to get help from wherever they came from.
Are we sure that opening the core is an ideal solution? It's the core of an entire planet. What would happen to Cradle if they ever broke into it?
2) The core is protected by a massive, impregnable shell. Nobody in the Spiral Order knows how to break it, and the people who are the most capable of assisting us are hostile.
So, we've already reached the core (as to why the knights still need to hack-n-slash their way through the clockworks after having already reached their destination still puzzles me), and we haven't really done much besides twiddle our thumbs since we got there. We're clueless as to how we're supposed to crack it, and the species most knowledgeable about the core (Gremlins) is hostile and uncooperative.
Ignoring the fact that there is an entire city of outcast allied Gremlins who'd probably be able to help, our only other ally (Strangers) is too busy making money off of us with their stores and auction houses to be of any real assistance.
3) Haven's currency - crowns - can be found virtually anywhere within the clockworks.
The Stranger's have a pretty successful business running in Haven, and have without a doubt become very wealthy from the knights that use their services. The only problem is that the main objective of the Spiral Order is to breach the core, and to get to the core a knight must kill limitless amounts of enemies along the way. That means they are capable of acquiring a limitless amount of crowns. This means that the crown is not a viable currency, and inflation should be plaguing everyone in Haven.
Despite the existence of a bottomless well of money that most call the "clockworks", the Strangers seem determined to continue charging the same amount of cash for their services today as they did the moment the Spiral Knights arrived. How they are able to charge such low prices and still run successful businesses is a total mystery, but who are we to question their flawless business decisions.
How do we even know there is a power source in the core?
Mist energy.
... everything we've done so far is based purely on assumptions, guesswork, and wishful thinking.
Sure. But it's been fun.
Also, why do we need to fix the Skylark?
Because building a whole new ship to carry tens of thousands of knights is far less practical.
I'm assuming nobody in the Spiral Order has ever thought about building smaller craft and sending a convoy of knights to get help ...
Sure, but that takes time, and SK is eternally in the time period a month or so after the crash.
... from wherever they came from.
And now you're assuming that wherever they came from still exists.
Are we sure that opening the core is an ideal solution? It's the core of an entire planet. What would happen to Cradle if they ever broke into it?
Ask Alpha team.
... an entire city of outcast allied Gremlins ...
Who might not know how to open the core any better than we do. Heck, we're not even sure that the gremlins are capable of doing this at all.
Haven's currency - crowns - can be found virtually anywhere within the clockworks.
This... I can't explain. But it sure is convenient.