Perhaps indeed, Notrium 2 could be something totally different... Naming it Notrium 2 might be a little misleading then.
I personally would like the original concept... But that's just me.
For a new planet (and possibly old Notrium, but I'd really prefer a new world) I have plenty of environmental ideas:
Different bodies of water, as MageKing proposed, with oceans and lakes having differing flora and fauna. And possibly rivers, mostly with lake flora and fauna plus a few critters/plants exclusive for rivers only.
For possible 3D, swimming in water should be rather free (diving about) and possibly races can swim differently: i.e. an alien would be quite adept at it whereas psionic will be quite slow and diving/being underwater should be rather hard. Androids etc. would have part of it easy, since they wouldn't have to breathe, but that could be compensated by them being unable to float, thus making them walk slowly along the bottom. Oxygen bar would indicate the obvious. Little oxygen = slow health loss. No oxygen = very rapid health loss (instant death wouldn't be all that realistic as it may sound).
All bodies water should be quite clear, mostly for gaming purposes.
Mountaneous regions.Gradually from open land with few trees to very narrow paths alongside mountains with nearly no cover from the drastic weather effects. Should you find a small incavement/a covering rock slab you can concider yourself lucky. Spots of climbable wall (just really slow walking + increased food consumtion) should be here and there too.
The top regions of the mountains (often covered in snow) should be hard for anyone that breathes; possibly the same oxygen bar could be used here as in water but it would never go beyond 'low oxygen'.
Underground. Yes indeed. I should be like another layer under the surface and perhaps with possibilities to go deeper into lower layers. Again, featuring very differing creatures from usual, getting more and more odd and scary the deeper you go. You'll find yourself in big trouble if your flashlight runs out of batteries... unless there are glowing fungi (preferably on the lowest layers) but even them shouldn't replace the need of your own light source.
Most caves though, should be very small, natural or creature dug caves not going beyond the layer right below surface.
Creature dug nests should be found randomly in jungles and deserts. Natural caves (which should be the only caves with a chance to go deeper) should be found in mountaneous regions and other areas boasting with radical terrain height differences (canyons in some deserts maybe?).
Non agressive creatures. Small, or just otherwise frightful critters that prefer to keep distance from player, some larger creatures which don't find you a threat and some predators. This would, though, kill the feeling that absolutely anything you run into will try to kill you, but it would include features such as you running into a running herd of some prey creature and find yourself running along trying to avoid being eaten by some huge predator for example. Prey animals would also make it slightly easier to get food. You should, then, include varying meats of which you have to learn whether they are actually edible or not. Some prey animals (probably those which are large enough) should turn agressive and maybe be more than enough challenge to bring down. Possibly the whole herd could then try to protect it's member.
Flying creatures would be one thing, but I don't have any ideas how you could actually make them and I don't see them all that necessary.
Seamless world would be very very nice. Though it may also be very very nasty for performance, especially with 3D. It may be very hard to code too... It's up to Ville whether to concentrate on a neat looking shell or rich and tasty fillings.
I'd have plenty of ideas concerning characters and backstory, but I'll leave 'em for another post.