Obsidian Entertainment designer Josh Sawyer has taken to his personal blog to spell out the reasons why he continues to dislike the way weapons and weapon skills are set up in the Fallout series (starting with the original up through New Vegas), and what he thinks should be done to fix the perceived problems.
1) In a game where a player makes an investment in a variety of skills, I believe those skills should be applicable from the beginning of the game to the end of the game. In F1, that wasn't the case with Small Guns/Big Guns/Energy Weapons. In F:NV, it was true for Guns and EWs, but it resulted in a lot of weapon role redundancy between the two skills.
2) I believe taking different skills should change the gameplay of the character. This really has never been true between Small Guns/Guns/EWs. You pretty much use all of them the same way, especially because of role redundancy or application overlap (cf. Laser and Sniper Rifles in F1, Anti-Materiel Rifle and Gauss Rifle in F:NV). It's also not true of Unarmed/Melee Weapons.
3) Not really my beef, but often comes up from other players: EWs in F:NV don't feel suitably powerful compared to conventional firearms. This comes from 1), where I wanted players in the early game to have access to items that consistently made use of their EW skill. Thus, you end up with Laser Pistols and Plasma Pistols that don't feel dramatically different from 9mm Pistols and .357 Magnum Revolvers. They're all starter weapons.
4) Again, not a personal concern, but an issue for many players: there are a ton of weapons and ammo types in F:NV. Even taking subtypes out of the mix, there are far more base types than in any other Fallout game, and an arsenal of weapons -- some people like this, some don't. My concern as a designer is that people are overwhelmed by the number of items and cease to be able to sort, distinguish, and make intelligent choices about what to use, and when. And the more weapons there are, the more difficult they are to balance.
I think there are a number of ways that you can organize weapon skills in Fallout. Based on discussions I've had recently about the above problems, I advocate reducing skill point pools further, folding more skills together, and cutting down the number of base weapon and ammo types. Guns and EWs become Guns, Melee Weapons and Unarmed become Melee, and Explosives stands alone (but absorbs Flamers, Incinerators, and like weapons).