Wow there's a lot to unpack here, so I'll just cover a few things:
I think more passive mobs should be added with their own unique functions for two reasons: populate the world with more diverse life, and make a player choose which animals to farm and in what amount, since farming all the animals at max capacity would become unmanageable and thus encourage a player to choose what resource they want more of.
Beavers would be a neat addition if they didn't have too much function. I think flooding rivers is a bit much, but it would be neat to come across a 1-4 block pile of sticks in a river (so found in river biomes only) with beavers coming and going from them like bees do with hives. What function would they serve? Don't know yet. But as a potential addition I like this idea. The dams would be able to hold back water, but water going over them would cause them to pop into a few sticks.
I don't know if we need any more mobs giving us items (villagers and cats for example already do this), but I don't necessarily think any mob needs to have a big new function in order to be considered. Bear variants that go for hives and cause the bees to get temporarily annoyed and drop the honey value to zero sounds reasonable to me. Birds that fly with modified bat AI would be another nice addition. They wouldn't do much of anything outside of making the world look more pretty and dynamic, but that's the point of most of the animals I can see being added.