Just skimmed your post Slim, didn't have time to read absolutely everything
But I like what you've got here, I think you've hit all the major points.
I think the animal ecosystem would be interesting (actually something I"m quite excited about exploring in RDR)
granted there won't be too much wildlife in a city there is always birds, dogs, cats, and possibly horses or farm animals at the outskirts of town. I don't see a hunting minigame like RDR making sense in a GTA but it would be cool and add to the feel of the city to see dogs and cats running around or people walking their dogs in the parks. I don't know why animals were never implemented before, possibly they didn't think it was worth the extra work but I think it'd add that extra something to the living city feeling.
The dynamic environmental weapon idea is cool too. Kinda what made Dead Rising interesting was the immense number of random items used as weapons. Also they had some basis for that in GTA IV already. You could pick up random trash and throw it at ppl, why not extend that to any loose object laying around, one button would beat a person with it and another would throw it at the person. Pipes, fence posts, chairs, anything could theoretically work for this.
Maybe I'll come back to this and add more thoughts but I've got class to head off to