Right. So what are the good or at least neutral differences that are lacking 4e?
Some of the issues you mentioned seem easy enough to fix: returning to monsters making "defense rolls" against the wizard's spells is a fairly simple change which does not really mess with the underlying mechanics of the system.
Some others are a direct result of the 4e philosophy that everyone should be able to contribute to combat. Hence, there are few abilities that are focused on avoiding combat and running away.
Others may be more complicated, but not impossible to add into 4e: for example, you could have a Skilful Rogue class feature (perhaps replacing Rogue Weapon Talent) that gives him a small number of bonus points +1 every odd level that he can assign to his trained skills to increase his skill modifiers.
I think one of the things I miss the most is the different ways of acquiring and using abilities.
Which means, for me, one of the more grievous similarities is "two at-wills, encounter, daily, then same advancement for everyone, always."
Which is, of course, the hardest thing to fiddle with in a balanced fashion.
But many of these other tidbits could go a long way toward making things distinctive. And though Prof C mostly hits on the noncombat angle, I think the salient point is something he articulated pretty well: I should be able to do things as Class X that no one else can do.
Where is the thing I can do as a rogue, or a wizard, or a fighter, that no one else does? It's not my combat role (others do that, though in different fiddly ways), it's not my out-of-combat role (others are basically my equal in this regard). What do I contribute to a party that is binary? That is "Oh, you don't have a Rogue, so you're going to suck at X."
I think this is a harder balancing act than even "power acquisition" rules, because part of 4e's philosophy is that everyone can contribute in some meaningful way all the time. Which isn't a bad philosophy, because it's boring sitting out a challenge you can't contribute to.
I dunno...there are some things that would alleviate the issue before we got to that point, I think. And maybe some sort of expanded roles system or whatnot is useful (In combat, a rogue is a striker! In exploration, the rogue is a trailblazer! In social situations, a rogue is a wit! The rogue is the only class with this unique combination; other classes have other combinations!) in just creating levels of difference.
The more things I can point to on my character sheet and say "I am the only character who can do
this," the better the class variety gets, I think.
Which brings us to the OP. I don't think this is an insurmountable problem for 4e. Heck, talking like this, it seems that 4e could even probably accept some add-on systems to mostly solve the problem. And those that don't have a problem don't need to use any of the sub-systems.
Hmm...brain churning...