I do not like Sawyer's view on design on an absolute level, and I find his examples kinda hit&miss, because they are taken out of their context. An option of Aboleth as a favorite enemy in D&D does not hurt the system, because players know what they would play and you can (or rather, should) give them an intro of where exactly they are going and what characters will suit the campaign. If we are playing the module "Orc Invasion in Kingdom of Derp", a player would do well to create a ranger military spy from elven forests who has orcs as favorite enemy and has a reason to be at that place and that time. This is common sense and roleplaying ethics, if player pays no attention to his build, or DM does't let player to take the spotlight when his skills should allow him to, in both of these examples people play one-way street. And as Hormalakh said, there is rarely a skill in CRPG which is completely and utterly useless.
From that point of view, a system with two skill pools does't actually seem to change the problem of their usefulness - this is not a solution, this is a crutch, because with two pools designer can still create suboptimal skills without thinking of how they will be balanced or implemented in the game, as he can always wave a hand and say "well, you have your combat skills, you can beat everything with combat". I find it perfectly fair one can't win Fallout solely on Gambling skill, but with right picks and skill combinations, Gambling can break the game, as you can outgun everyone by spending money on weapons and armor for yourself or your companions. I also hold strong belief that in a postapocalyptic world of bloodthirsty raiders, radiation-gone crazy robots and mutants one cannot, and should not, survive with Diplomacy only, just as talking down a few random schmucks who want your wallet is rarely a possibility even in relatively safe "real world". Figuring out a skill set to survive in game world seems like a problem worth solving for a player, no?
But "rogue" thing is one I dislike the most. You see, some people prefer combat, some people prefer social roleplaying. Some are fine to suck in combat a little, some see no trouble to say "Well, my 16 years old daughter of herbalist hides until combat ends" and go make some tea, while others indeed can feel miserable because they do not understand the system and want to play something else. So I've heard, some believe that making every class combat-competent is a good thing in 4th edition. Although what's the point, if most people who do not like combat I played with just don't like it even if they win? They will still avoid combat just because their characters would do so.
But in CRPG noone will feel useless, because you command six characters and I never ever will understand why one or two of them can't suck in combat but be competent in everything else. I had no trouble with my diplomats in Fallout and Arcanum taking almost no action in combat, I had my companions for that. And after combat, a healer-companion could patch them up and we're going for next encounter. What is exactly wrong with that? Why can't I have a social-oriented characters? They are not human, they will not shout at me cause I don't give 'em enough spotlight.
And now I will explain why everything I wrote is completely pointless and why I don't actually care about that in P:E. Well that's because P:E is supposedly an Infinity-engine successor, which means it's a game based on combat and about combat; that's the reason there are classes, which in most of games out there are too, just about combat and combat roles. It's not a simulation-based world, thus I don't care.
(But if, IF Sawyer would defend the same system in a simulation-like world by trying to partially shoehorn every character in combat skills, in a game where picking a set of skills to beat it in a unique way is the point, I'd call bullshit).
1. How is reading the manual supposed to let me divine that I won't get Energy Weapons until the late game?
You are in a bombed world where everything is shit and people fight with spears. Take a hint?