I think one needs to step back and reazlie that in a game that tries to be as diverse and to allow as many archetypes as D+D does, some of those archetypes simply will not work in conjunction with each other. Paladin and (known) Assassin in the same party? Not unless the circumstances are truly bizarre. But don't ban one or the other...let 'em fight it out if it happens!
That said, there's been some restrictions that haven't made sense from either a flavour or mechanics perspective. Example is the 1e Ranger: they had to be Good, and no more than 3 could operate together. This has no mechanical impact, and flies in the face of flavour (why can't a mass murderer on the run learn woodscraft just as well as anyone else?). So, out said rules went around here, a long time ago.
Prestige classes were a disaster in all ways. 'Nuff said, except I'm glad someone else seems to think so too.
As for Thief/Rogue being useless sometimes...again, it comes back to the simple fact that not everyone is going to always be the perfect tool for every job. A good example is the 1e Illusionist, or any-e Illusionist, in an adventure that is all undead. Or a Druid in an adventure that is all underground. I don't see this as a design flaw in the slightest; just a logical reflection of reality. the flip side, of course, is there'll be times when the Illusionist (vs. dumb Orcs or Giants) and Druid (in an outdoors adventure) just rock. And Thieves can do much more than backstrike...just make sure your DM is giving you ExP for the locks you pick and the gold you steal.
A bigger design flaw would be a class that is useless *all* of the time. 1e's Monk was close to this at anything less than high level.
Hussar, it's interesting to note your take on Haste...you say it was "problematic" when it had a risk of killing you when used, but that was the whole point...it had a drawback that made it risky to use, and thus it wasn't used except in dire need, as designed. Take away that drawback and of course it becomes broken...but the solution is not to nerf it, but to put the drawback back in! Same is true of Polymorph...it only broke when the drawbacks were removed (that you could only poly. yourself, or for Poly-Other you had to make a system-shock roll and even then might truly become the creature you'd been turned into, and NOBODY would willingly undergo this).
So, I suppose what I'm saying is that the rules can be designed around the flavour, and should be where it makes sense. Don't design for "what happens at the table"...let the players figure that out, and design for "what happens in the game world".
Lanefan