Why do you accept player skill in playing and not in building? What's the difference?
Second, I don't think player skill should ever matter. You build the character you want within the rules, and he might be effective, and he might not, but then he succeeds or fails based on his merits, not yours.
Building the character shouldn't require skill. It should just be an expression of the player's preferences for that character.
If you build the character the way you want to build it, and you play it the way you want to play it, then you win. That's the only standard of success that matters in a roleplaying game: Did you get to play your character the way you wanted?
I like suboptimal options partly because they are options, and I want options. But I also like them because I want the game world to be credible, and if the only skills available are the ones I can use to deal with this specific threat I face, then the game fails that test.
Gamist design is bad design.
I agree it takes no skill to make a character.
What you are describing is more or less what I am describing though, building the character you want to build should be the point. But if you are going to be punished by the system for building a character that doesn't fit within the paremeters of what the designers THINK you should build, then the possibility of having fun diminishes. The standard of success is not playing the character you want to play, such a thing is too narrow of a definition.
The standard of success is how it plays. If you are in a game where a sub-optimal build is discouraged, you may not have fun in that game. Likewise if you are power gaming it and people get annoyed at you, including the GM.
And to be honest, what you describe as being positives is moreso gamist design; its part of that insider baseball of "I know these options are better than others, so let me take them because I want to be effective at this only." kind of attitude that is bred through such mechanics. It is players pigeon-holing characters completely into a specific role, which doesn't really play as much as it did back in the 1980s.
Even games like Pathfinder now focus heavily on cross-classing and unconventional builds and feats to accommodate odd design choices; there's official rules for a fighter to be captian ****** america, using a shield as a boomerang now.
That speaks volumes to me, honestly, about how open a game like Pathfinder can be about options, while simultaneously doing its damndest to balance them out. Not perfect (Summoner is fairly OP if you use it a certain way) but you see it in its design. It is not about how skills deal with specific threats that makes them balanced in any way, sub-optimal options exist for everyone depending on the type of character you build; my rakish rogue from before could have invested in stealth and lockpicking, but I chose not to because he is not that kind of rogue.
It should be about how you use such skills and abilities effectively. Anything purposely sub-optimal though is a waste of time and energy.