While there are many thing within the Clockwork that irritate me, there have been two things that are just out of place:

• Why do the inhabitants of Cradle get along with each other?
• What are they doing on that specific floor?

The first one does not just include Wolvers and Chromalisks not eating each other, but further question,why the hell is there a Gremlin among a pack of bloodthirsty Wolvers healing them? If there was some kind of backstory, where Gremlins actually have farms where they breed savage beast, then that would be another story, but right now, this makes no sense. Also, Gremlins don't look like farmers to me. Which also sparks the question, what do all these races eat? Appearently not each other, so what else is left?
Further more, the Gremlins sustained great facilities to produce weapons and the constructs we fight today, but long before the Isorans ever set foot on the planet - what where they defending against? Maybe the Swarm, but given that it's influence is very restricted one may doubt it.
Also, the phenomenon of Cradle races getting along is not limited to beasts, but also to our friends; except for the Wall around Haven, there seems to be nothing in the means of the Strangers that they could use to protect themselfs. The wall doesn't even have door they could close. I'd say that's due to the fact, that it's not for actual defence, but rather to keep the city clean from monster feces.

The second point is, why is there anyone on that specific floor? While it may seem self-explanatory, this goes beyond the simple why is there a Gel in a Gremlin facility. Sure, that alone is a thing that has to be explained, but there is more: Why are there sentinent beings like Gremlins scattered about a floor where there is absolutly nothing of relevance? What purpose do the immovable Battlepods serve if they are placed within Gremlin territory? Why do they pose such a threat to us that we have to destroy them in missions, if they obviously can't move?
...Though by now it's quite obvious that the Isoran race gets their kicks through violence and destruction... No one sends a giant flagship filled with armed soldiers just to scan some planets and maybe find some new merchant-routes.

The suggestion at this point is as simple as can be:
Give us a story. And I mean an actual story, not a mission description.
Also, make the enemys attack each other at times. Can't be we're the only ones to get all the hostility.

This is not to say, that we don't need a lot (A LOT) more story in this game, but this is a matter right at hand.

UPDATE: Why the Swarm does not explain any of this

The Gremlins are a stand alone race, not some special and deformed individuals. They formed and maintained a working social structure in which they act under orders of their superiors. Arkus was able to do nothing of this, having been driven into isolation instead. On the other hand we have Vanaduke and the Empire of Almire which most likely fell prey to the Swarm of some sorts: His madness and land share nothing with the culture of Gremlins or demons. Also there are the Emberlight Gremlins, that chose to be exiled out of their own will, interacting with other races peacefully.
Monsters grow stronger as you go deeper, true, but the same holds true for you as a knight as well, doesn't it?
Furthermore this all is not limited to the deepest depths of the Clockwork but present even on the surface. Also we still have to deal with the fact that Strangers don't seem to actively protect themselfs from any of those threats, probably even being part of the system.

Given that everything except for constructs are organic beings we would still have to explain what they eat. At least the Wolver species is somewhat verified to procreate, as there exit "cubs". Same goes for the Jelly family, that seem to have male and female individuals. Being powered by the Swarm wouldn't work then, because it would lead to an overpopulation of the planet. Infinite "food" resource, no natural predators, and, if it's the Jellys, high number of offspring. That can not work.

The Swarm could corrupt them, like it does in the Unknown Passage, but it does not explain Gremlin culture, procreation, a free will, levels close to the surface or survival and death in the Clockworks.