I detect a note of MMORPG in this, and while I am against that topic due to the MMOG mechanics interfering with basic CRPG aspects, not to mention what makes Fallout so dark, this topic does have some merit otherwise.
Regardless of that, and back on topic...
The best way to make a world come alive is to do as others have pointed out, by a proportional system. I would have to add that it would be much like real life, but with the science fiction twist to it.
So...I'd guess you should take some wildlife statistics from the area you're going to "nuke", then replace species that might not have made it with mutated critters, adjusting accordingly for their new state (Radscorpions now reverting to the size of the great sea scorpions of eons ago), then twist the ones that would have made it. Even 80 years after the Great War, wildlife will have still flourished, but will have lessened quite a bit due to scarcer food. So then take those figures and drop them down a bit more. Then, make some species extinct, especially if their food supply doesn't naturally thrive or if they don't have the skills to fully scavenge in a post-apocalyptic wasteland on their own.
Next, any critter inclusions should be rather dark, feral, and suited towards the post-apocalyptic world. They should also have a 50's sci-fi bent to them, and a background of some sort is preferable, but don't overdo it with a new mutation coming from a new flavor of toxic spill. They should also fit the location, for flavor purposes.
These are in no particular order, but it is to demonstrate their position in the Fallout "ecosytstem" and how it parallels our own, to give a bit of background so that other critters may be included in similar style. Also remember the differences between FEV mutation and radiation mutation. MCA even hosed up the "Fallout Bibles" with that (which is generally why I didn't waste my time with them, because the lead developer for Fo2 was clueless even years after developing the game), in saying "Creatures not mutated by FEV probably did not survive the aftermath of the Great War, with the possible exception of cockroaches... and perhaps normal ants, though there are FEV-infected versions of these species."
I guess MCA forgot the part in Fo1 where FEV was not airborne, but had to be injected or immersed to have any effect. Or that "radiation + FEV = death", as stated by...well, damn, even Zax itself, not to mention just about every FEV research tape found.
Oh, and that the FEV experiments were moved to the Military Base
before The Glow got nuked. Or that the presence of the FEV wasn't until relatively recent in the Fo1 timeline, as Harold and Grey didn't go into the Military Base and become separated until long after the Great War. It is also highly doubtful that creatures that wandered into the base and became mutated managed to wander miles away and widespread into human presence, like the brahmin, or even to the population of the other wasteland critters.
Cockroaches = Well, maybe not well known in the 50's, nothing screams post-apocalyptic like these suckers still crawling around. Of course, they will mutate, and 1/4 of the population exposed to radiation will die off, due to being in the molting stage (and therefore vulnerable through split cells). They will still be plentiful, and will likely be found wherever there is dead.
Rats = Plentiful, and generally how they are today. They also take to the ground and tend to have a good sense about their surroundings, so aside from a few at Ground Zero, I doubt the common rat population would go down. They would still inhabit around human dwellings first and foremost.
Molerats = Radiation made these critters bigger, and in the general representation of the species in Fallout, they are like your medium-sized land predator, much like the wolverine or fox's place in Alaska. They still have the preference of the original species, to live in the dark and relatively near humans. I would say one of these for every hundred common rats, and varying for each flavor of mutant rat.
Dogs = Perhaps the only untouched animal in the Fallout universe besides the common rat. It seems like about 1:50 dog:human, although some places might have a lot more given hunting preferences.
Mantis = Perhaps similar insects like them could have survived and mutated, and I would even hazard a guess that like the brahmin, some herbivor insects may have survived. You would definitely see a lot more insects in the wasteland afterwards, because they are more resiliant.
Mutant Venus Flytraps = Befitting Fallout, as this was a favorite toy plant for many people and classrooms in the 50's as a supplemental science teaching aid. Though, personally, have no damn clue how they originated in the Fallout universe, other than possibly a nursery got radiated with fertilizer and these things sprouted out.
Geckos = Similarly showing the signs of both radiation mutation and Fallout's brand of sci-fi, in which the critter becomes overly aggressive.
Wanamingos = Please just call and treat them like giant mutant ants. Please.
Brahmin = The population is severely less than cattle previously, as the radioactive twisters miles wide have turned the cattle pens into the world's first and largest cyclonic neon barbecue, but about 1:5 to humans sounds right for brahmin in a farming community. I doubt you will find them elsewhere except for caravans.
Radscorpions = Much like their normal counterparts, they tend to seek the dark places to hide, and may tend to be rare, surprisingly enough. You may run into them quite a few times in the wasteland, but with their body mass and preferences for caves to hide themselves in, they seem to be limited in where they live.
DeathClaw = Grizzly Bear/Wolves, pack mentality and a great predator, even over mankind.
Mutant Army = These freaks are made from everything else, apparently, and only come from one source. I'd say they should be limited in region, which seems to be a few square miles around the Military Base.
