Oh, these questions are always interesting when there's some support to the answers, especially as part of the official texts and images (although some non-canon info might also be interesting because of Werivar).
I haven't put that much thought on the look of the creatures in the game, but its top-down perspective suggests that the blue alien is quite similar to those seen in the "Alien" series (but as you stated, with different hands that would mostly serve as claws and make it unable to perform complex tasks such as wield weapons). As for the player's alien (the female stowaway, also called Nuaq at some point, though I'm not sure if it's official), it simply resembles a mixture of both the blue and the brown alien.
The part where combining things would produce more weight has bothered me as well. But I must add that most of the time, such objects become unbreakable. If one would like to make this sound reasonable, I'd start with the combination increasing the mass due to relying on other metallic pieces found abundantly on the planet (although this doesn't justify why the player just stands still in the process).
The food generator is a somewhat reasonable part of it. Once we have a replicator cell that can generate other molecules out of thin air (or other sorts of fuel), all that's let for it to produce an edible portion of ration is the software to program the right behavior (telling it to generate proteins and other nutrients). Given these assumptions, the 10 units of ether required to generate one ration is only the fuel.
But there are also some interesting behaviors for the ether tank. Picking it up is followed by a description that the container is made of a very resistant material, also claiming that they could have been brought to the planet from the ship itself (the Var' Equinallin). The replicator cells are most likely a familiar technology, which is why they had so many containers: to fuel the food generators. There's even a food generator chip in the escape pod, in fact.
As for the energy unit, besides it being used to charge the player's batteries, also seems to serve as a voltage amplifier. So rather than providing energy to sustain itself, it augments the power of some items such as the diode. But you're right, sometimes the energy unit is used to make self-powered items (but is mostly non-canon because of Werivar, I'm not sure if there's such case in the default mod) and structures (the stasis field). In addition, some things cost ether instead of energy (the propulsion boots and the hoverbike). It sounds a lot like the thought of making another kind of item for amplifying the effect of another would increase the complexity a bit too much.
The part of the turrets lacking some precision actually makes sense. Althought the laser pistol fires a straight laser burst, the motion detector equipped with the turret might not be that accurate. The player's laser pistol isn't 100% accurate either, but that may be assumed as a flaw from the character wielding it. The sniper rifle is a bit more accurate, at the expense of lubricated bullets and a lot of recoil.
That's all for now. Let's keep them coming.