I think that when people begin to over-analyze the game of D&D they risk ruining that in which they care to play under whatever guise they are speaking on. This holds true in my mind about this thread when speaking on the problems that 3.5 are said to hold by the original OP and many others including myself at times.
When playing a character based game that such characters have some overlapping abilities but for the most part have very different ones there should be "x" values in which each different character, due to their skills cannot attain. Just as due to customization some of the same characters decide not to attain though they very easily could have. That is why this game has many members to each party, and even with the regular 4 to 6 in a party the group may still have trouble or even never be able to figure out every part of the game in question. That is where the builders of the modules and/or the GM come into play to find and make things work, many times on the fly. That in and of itself is one of the core aspects of RPG's and that should never be forgotten.
Heck, when they send a group of Astronauts into space do they send them all with the same skills, or do they all have some skills that overlap with most having totally different skills for obvious reasons. This is one of the reasons in which I enjoy 3x and due not want it to change.
While I don't disagree with this, I think you may not be understanding why people are making these claims and grievances. There are definitely different skills that everyone can do here - wizards cast spells, druids communicate with nature, fighters generally triumph over things by stabbing them a lot, etc. And we all do enjoy role playing games - that's why we're here discussing them!
The problem is when one skill becomes so great it actually strips the skills from another through outclassing them (the issue between melee and wizards). Or when players are at the lower levels and have skill differences that make every class unique, and more importantly create a balanced and fun playing field, and then these skills become grossly unbalanced due to a flaw in game mechanics (the first point Matt brings up.) When flaws in the game make the game become NOT fun to play, there is a problem. And when these problems have a chance to be fixed, especially when there is a publisher that wants to (or at least gives the illusion that they want to) collaborate with players to fix these issues, that's why they're brought up here.
If anything, all this is because we love the game so much we want to make sure we can attempt to perfect it.