I am playing Notrium for some time now and I still like it.
Maybe I can give you some inspiration due to my experiences with Notrium.
Some of my proposals were a very fundamental change others are just lesser improvements.
Don't be angry with me, because they are many.
1.) An 3D environment.
2.) A more dynamic environment
3.) Yes, water (with creatures, maybe) and thirst
4.) More different kinds of creatures which might provide useful ressources, too
5.) Building (or repairing) structures
6.) Planting seeds (includes growing plants)
7.) Some more different sources of food (fruits e.g.)
8.) Containers to store items
9.) Manufacturing items
10.) Nice new weapons
11.) Better graphics for a few items
12.) The possibility to communicate with some of the NPCs
13.) A better artificial intelligence
14.) A more realistic computation of the items' weight
15.) A construction menu and (customizable) shortcuts
16.) Buildings should give shelter against the rain
17.) A highly customizable degree of difficulty
18.) A well-designed useful journal
19.) When achieving a goal there should maybe the possibility to play further (depending on the situation)
2.) This is naturally a wide field, because it includes some other points like the structures, plants and animals. But this could also be almost everything, for example something like deformable terrain oder new radioactive areas.
4.) The only "animals" which deserve this description are just the aliens and these just divide into about five main groups (the queens do not even respawn). I like the design of the aliens, but maybe there are a lot more possibilities.
5.) Building an own base or camp is rudimentary realized with the barriers and the turrets, I think, but it's a very interesting point which developped further. I also think of Hermit's house which is destroyed at the beginning of the story or some other ruins which could be rebuild and be used. An idea would also be the construction of traps which could trap or kill animals.
6.) How can I say that? The Fungus as a plant sometimes seems to be too static and doesn't seem to grow naturally but to lie around like a fuel cell or something, very sterile for a plant, and the healing and the electric plants, too.
8.) It's just a little bit annoying and a waste of space when all the items you collected are lying around. For some purposes, for example to store ammo or food or less needed items I'd wish to have a container for.
9.) It's a little bit boring that the almost only way to get useful things is to find them on the map. Sometimes it would be nice to manufacture (like the barriers, generated food rations, ice packs) more of them. For example to mine or search for ore to produce some of these nice long metal rods.
It would be also an idea for a new location: an abandonned factory which can be used to produce fuel cells (which could be rarer items on the map then).
The Firewood could be collected or manufacturend from certain plants for example, too.
10.) It's something one can made very much proposals for that: grenades, mines and bombs, hand weapons for close weapon with different properties, electric weapons which might interact with wather ("dynamite fishing") and so on.
11.) Something I didn't like: the warp gun doesn't have proper graphics and the ammunation for the sniper pistol is just too small to drop them. That's annoying, because the sniper bullets are heavier than the common ones.
12.) It would just nice to have more of a role-playing aspect in notrium (which rather seems to be a third-person-shooter sometimes).
13.) Related with the point before, it would be interesting to see the marines for example working together and walk in formation to catch you once they spotted you.
14.) It was just said before. Usually, any item combined of other items cannot be heavier than it's components (with exceptions, yes).
15.) There are some objects which you need to build more often (rapid fire pistol, laser turret, force field generator, sniper bullets) and which cannot be created comfortably by the current system. There could be a menu with the discovered combinations where you can instantly build the wanted object and maybe there could be two or three customizable shortcuts you can use for the most needed combinations.
16.) It's remarkable that Hermit's house doesn't give any shelter from the acid rain, but the trees around the house do.
17.) Sometimes I was a little bit sad that I cannot customize the degree of difficulty like I'd like to. For example, I'd like to play with the weather effects like rain, but without these immense changes of temperature which make the games so hard.
18.) The current journal just tells a good story (I like it), but doesn't provide information in a good way. In a better designed journal there could be information about the locations, animals, structures and weapons and maybe even space for own annotations.
19.) The best negative example I can give for this is when killing the alien queens. You have to take care that you or your minions don't destroy the eggs because this ends the game immediately.