In fact in the original premise I state CLEARLY that it's WotC and 3E that fucked things up. I gave the example of Midnight using Persuasion, although she's a Wizard class character. That would work under AD&D since AD&D didn't have a formalized skill system, so you would just make some sort of Charisma check (or rather, the target would make a savings throw roll vs. Midnight's CHA score).
OK. This is getting out of hand.
Midnight was a wizard with a high Charisma.
1. She could use Persuade/Diplomacy UNTRAINED.
2. She could put points into it CROSS-CLASS using the COPIOUS amount of skill points wizards get because, get this, their casting stat is INTELLIGENCE.
There is nothing preventing her from using Diplomacy, ESPECIALLY if she has cross-class ranks in it.
In fact, there is nothing in 3.5 that prevents you from taking cross-class skills so long as you have the skill points for it. It is better than 3.0 in that regard because 3.0 DID have class exclusive skills (Use Magic Device, for example).
A class gives a set of general abilities that makes your character more inclined towards one something. There is nothing preventing you from making your character do something contrary to that. Prestige classes allows you to refine where you want your character to go. For example, if you want to make a Captain America or Thor type character, you can take levels in the prestige class Bloodstorm Blade, whose class abilities revolve around throwing melee weapons (which includes large and small shields) and getting it to return to him. A basic Fighter cannot do that.
You are putting far too much emphasis on the bloody label and not understanding the fundamentals of a RPG: Every single stat, class, skill, save, BAB, spell ability, special ability, WHATEVER! is but a tool to create YOUR CHARACTER. The one you want to play. It can be Thor, it can be Robin Hood, it can be Galahad. IT DOESN'T MATTER. That is the beauty of the 3.5 class system. It is versatile. It can be broken down to abilities. It can be customised to suit your needs. I have even made an approximation of JEDI using 3.5 DnD rules.
To wit:
I am not a fucking Fighter/Mage/Eldritch Knight/Spellsword/Abjurant Champion, you blithering imbecile!
I am Valerian Nammarie, Champion of Tura'Ithiron, Knight of Leaves, Defender of the Queen and your death, vile ravager of the Grove of Armonia!
What WotC fucked up was 4th Ed.