When Fallout was converted over to the SPECIAL system, Chris Taylor and a lot of the other team principals had to rebuild the weapon systems from scratch. Chris worked up the systems for damage thresholds, AP, and so on, and many people on the team contributed their ideas on the use of various weapons.
The initial design goal -- as I recall it; Chris T. might have something different to say about it -- was that each weapon skill group had its own rewards. If you tagged Small Guns, you had an edge right out the Vault at the outset, because you could certainly kill those Giant Rats and Mole Rats much more quickly. If you tagged Big Guns or Energy Weapons, you were taking the trade-off of a slow start in exchange for a long-term payoff. Remember, this was '96-'97, so there was still some debate about whether all builds should be equally viable or whether some builds had specific payoffs that might give you other hurdles (for instance, if you tagged Lockpicking, Gambling, and Outdoorsman, you were probably setting yourself up for a very difficult game with a few shining moments of payoff).
As we approached the end of the dev cycle, it became apparent that some weapon classes were just not keeping up. My stock testing character was an Unarmed/Speech/Science build, and obviously I just couldn't keep up with the endgame encounters while totally unarmed. This sort of testing triggered the creation of "unarmed weapons" such as the brass knuckles, spiked knuckles, and eventually the power fist. This was intended to let the character have an advancement track that would keep up with the enemy power curve. Its success is debatable; clearly when you're fighting centaurs and nightkin, even using the power fist is often a very tough row to hoe, and you rely on a lot of critical hits. Of course, unless you take the right perks, your crits are not guaranteed to do a lot of extra damage, so you may find yourself saving and reloading a lot!
Small Guns had several weapons that were certainly more viable for your endgame play (sniper rifle, .223 pistol) but obviously it wouldn't match up to a lot of energy weapons (turbo plasma rifle) or big guns (gatling gun, rocket launcher if you're feeling saucy). You were getting an immediate payoff for tagging Small Guns but this trade-off would haunt you later unless you slugged away a lot of skill points into skills that you weren't going to be using right off the bat.
I'll admit, the first time I played Fallout 3 and a mercenary dropped a laser pistol right outside of Vault 101, I was pretty surprised. I wasn't expecting all weapon classes to have representatives that ranged from the low end to the high end, thereby giving each weapon category a full scope of playability. It's an interesting design decision, and given the size and scope of games today, probably a better one -- the player doesn't become handicapped by a skill choice, but rather has the option to use his/her chosen skills and sometimes will discover that those skill choices provide extra special bonuses (if you happen to have a weapon that's very good against a particular enemy, for instance). This is harder to do if the player tags no combat skills, but hey, in that case the player ostensibly knows what he or she is getting into . . .
Anyway, that's all that I meant. The weapon skills in Fallout 1 were not designed to force you to spend a bunch of points on Small Guns, then have it become obsolete and force you to spend points on Energy Weapons. Rather, the choice was whether you wanted an immediate payoff or a later payoff. (Whether this actually succeeded in its design is a matter of interpretation by the player. I know that using Unarmed Combat in the endgame got pretty tedious for me.) In modern game design I'd say it's better if whatever your skill choices, you get SOME kind of payoff at each stage of the game, so that you have a more uniformly positive gameplay experience.
