Class fantasy changes were needed because Blizzard strayed too far from the actual fantasy of each spec. Seriously, what the fuck is a "Combat" Rogue, and why did Subtlety hardly ever use their Stealth abilities outside of a cooldown. Why were all Hunter specs almost identical, why did Demonology move from a pet based spec to a spec that turns you into a demon, I could go on.
Ultimately, you can't expect a complete rework to fix everything in the game. In fact it's the opposite, tons of problems arise when you rework everything. The point of the reworks was to make a clean slate so that they could build on the classes properly.
And I disagree, classes/specs definitely feel more unique than they did in the past.