What I think would be cool to see in FO3 is reuse of a few of the things from FO:T (Which I think is damned good for what it is, just not a traditional Fallout).
Giant wasps, cockroaches, the bigger spitting roaches, these things were pretty cool. They also added a nice layer of variation over the 'dogs, mantis , scorpions and rats' thing you started to run into a lot.
Also, the addition of 'normal' lizards in FO:t was pretty sharp, as they weren't anything really odd (Massive scorpions, or oversized rats) but added a bit of flavor.
The beast masters were interesting, although not all that amazing. The idea of a group using animals along with normal weapons is good. Like said earlier, raider packs with trained dogs on the side.
The Reavers were cool, they fit in with FO, but seemed like they could've used a little more work (Rags and leather for a group that worships technology?).
The hairy deathclaws were weak in my opinion. Old FO1 DCs you could be proud of. They were just menacing enough without being overboard.
Now, moving away from FO:T I could see things like snakes, spiders, some birds, bats, things like that. Not all of them huge, either. Some a little bigger than normal, but not 7 feet tall. Or at least, keep them rare.