I'm seconding worms and birds, both could be taken in very interesting directions, as enemies or, mostly for the birds, just background stuff.

Honestly, I want to see a big variety of robots.

see anything you like?

The Fallout series can pull off robot models really well for a game like Fallout, so I can't wait for some Robot model concepts for V13.

I want to see realistic behavior in NPC mobs. If a coyote comes across a pack of rabbits I want to see the coyote try to chase and eat the rabbits

Would be neat to see if that kind of AI is possible. MMO's... MMO's never change...

It'd be cool to see more robot dogs, I love me some robot dogs.

I want to see the badgers.. Personal opinion of mine. I just want them.

Killer Death Bunnies!! With Giant Teeth!!

"I *warned* you, but did you listen to me? Oh, no, you *knew*, didn't you? Oh, it's just a harmless little *bunny*, isn't it? " - Monty Pyton's Holy Grail

wolfs, snakes, birds, apes, zebras, panthers, every exotic animas, but not only this.
maybe big foot, yeti, treeman (like fallout3), antropomorphic things, cockroach-humans, etc
new "things" stranger an incomprehensible, some like centaurs, things that make you vomit,
and ALIENS!!!!

Big cats...some mutated snakes...and what MMO is not complete without freakishly large spiders..RADSPIDERS! Wolves! If dogs made it I would think that other canids would have as well. Flying beasties as well..Bats..Manbats! Some water creatures too..maybe gators..eels..mutated snakehead fish. Mutated Fungi and Plants. Androids!

Mud dauber wasps - With the largest specimens, you would run the risk of being paralyzed, flown to an egg chamber, and sealed in. You regain enough movement to give yourself an adrenaline shot, just as the eggs are hatching. Now bust out and fight your way home... or, it happens to some kid and you have to rescue him, whatever. (not as fun)
trap door spiders
semi intelligent tribal raccoons - Skittish, not normally hostile, scavengers with a den full of random crap.
vultures
more non suicidal creatures like ambush predators and sneaky hunters Don't tell anyone about this!

I've got the perfect thing for a Fallout enemy: Mutated giant snakehead!

It's a fish... but it can travel on land!

And being mutated, it could pull it off with bloody results. Imagine: a wanderer travelling by the river is attacked by a giant, mutated fish. He escapes inland, thinking he's safe. But the fish doesn't think so: It simply slithers ashore and resumes it's assult with renewed vigor. A deatchlaw of the waters.

Here's the most ferocious picture I could find using a quick search, I am not sure if it's the exact species I mean, but gives the idea:


http://un2kmu.files.wordpress.com/2009/10/giant-snakehead-teeth.jpg (where the pictúre is from)

Of course, multiply it's size by about a hundred.

I would like to see a human faction that is hostile to everybody, some kind of chinese spy base in the U.S territory (it could be bunker so it was not affected by the radiation). We have the Shi in FO2 and a radio station that broadcast chinese propaganda and all the weaponry left by the chinese in FO3, so it's canon. Lok'tar ogar for the Horde... man I love WoW...

raiders?

F3 is a rare fail from the point of matching the setting. Nowhere in Fallout 1-2 were said that the war was against the China. Besides, just think: if america had a war with Cina, how could th Shi survive in SanFran? They would be ripped out.
And what spies may be after 200 years of the war end?
As Bikkebakke said raiders are hostile to everybody. And slavers will not loose a chance to get new slave if they will meet you alone. Enclave troops are hostile to everyone, who is not belongs to Enclave. Wandering supermutants from the Master's army are not friendly too. And so long. Excuse my bad English... I am a Russian bear, it's hard to type with claws.