I agree that, if possible, the spooceshrubs could do with a new model, or at least perhaps a more muted, darker texture.
Yes, they are an in-game collectable, but they are supposed to be a part of Oddworld plant life that the characters are aware of. Contrast this to typical game collectables (coins or whatever) that are pretty much superficial for the player, and not considered a physical part of the character's world.
I just feel that the spooceshrubs are so bright and abundant that not only do they not look like a natural part of the environment, it also somewhat ruins player immersion. Instead of being able to appreciate the aesthetics of the landscapes (I actually think MO has a pretty decent colour palette consistent with the older games) the player's eye is constantly bombarded by bright green blobs. At some points, the levels look more like a maze of green balls than they do an Oddworld forest, etc.
If they could be changed to blend in with the environment a bit more- not to become invisible, just so that they look like a natural part of the landscape- I don't think people would mind the whole concept of spooce as much. If it looks like it belongs in Oddworld, people will no doubt accept it as being a part of Oddworld. If every spooceshrub screams in your face for attention as they seem to now, they become annoying! I think having several different models to increase variety would help greatly too.
On a separate note, I know Glitch has said that environment geometry might not be able to be changed. If it can however, check out the video below at 29.45- The door opens and disappears into the floor, but there isn't actually a space for the door to fit into!
http://www.youtube.com/watch?v=qcKn69hOvrE