There are some changes to specific mechanics, they definitely streamlined stuff and tried to make some of the core mechanics more intuitive in 3e. But the characters largely operated on the same principles. Fighters hit stuff, wizards drew from a large selection of spells.
I think that last part is a bit carefully-crafted. In 4E fighters still hit stuff, and wizards still have the largest selection of powers, due to their spellbook feature. You might not think that it's "large", but it's still the largest.
i could see the progression of thought from thac0 to bab, and to bringing most rolls into the roll over on a d20 mechanic. Things were opened up a bit as well (for instance putting the thief skills into a general skill list that everyone had access to).
Again, just because something is easy to understand does not mean it's not a significant change. A change with a good reason, perhaps, but still a change. Since the introduction of the thief class, only it had a skill list like this...but applying it to all characters is not a big change, to you. See comments below.
But it very much felt like D&D. Go to 4e and suddenly every class is built around the same exact resource management scheme.
If allowing everyone to have skills is not a big change, surely giving everyone the same resource-management scheme is also not so big?
Previously, the skills set the thief apart from the other classes. That was taken away in 3E. The per-day spells set the casters apart from the other classes (except, to some extent, the other classes that had per-day abilities, since we're talking resource management). That was taken away in 4E.
Moreover, 3E put every race on equal footing. Any race could be any class and go up to any level, which is of course very different from 2E. There was no such thing as a non-human paladin in 2E. They simply didn't exist. In 3E and 4E, they're all over the place. Move beyond thinking just about classes and you realize that this is an enormous change in its own right.
The spell system is completely changed.
It certainly didn't survive unscathed between 2E and 3E either. How many spontaneous-casting classes were there in 2E? The 4E change to spellcasters is bigger than 3E, but that's not the only factor to consider.
As for healing, 3E had a pretty big change there as well in the form of the
Wand of Cure Light Wounds. So even though the spell system was pretty close, the item crafting system was entirely different and had a huge impact on play.