3e changed the basic mechanics of the game. Everything became d20 + ability score + modifiers. It was a very big shift.
That's not a change, just a consolidation. The d20 had always been the most prevalent resolution mechanic, 3e just took it and made it consistent. A step forward, certainly, but not a radical one.
There were a few continuity changes in the mix though. Eladrin being the big one. Primordials. The Dawn War.
The Eladrin thing had two sides to it. One was the Cosmology issues - there were no longer alignment-based planes each with their own species of Outsider. The other was the naming of elven sub-races. The original Eladrin were more or less defunct along with the grid they were filling, the name was re-cycled for the High Elf (and ultimately sun elf &c), and Elves became wood-elves. (Drow stayed Drow, more or less.) Doesn't seem like a huge continuity issue. Not so much what was there, as how it was modeled.
Now, the rest of the Cosmology was interesting. Sure, they're obviously different in presentation, but there are also similarities in kind, and a lot of the differences could be viewed as seeing the same beyond-human-conception things through different filters. (The way Planars and 'clueless primes' saw things differently in Planescape, for instance, though without the assumption that one was definitively right and the other merely ignorant.)
Or it could be taken as being in different epochs.
The original elemental planes, for instance, were a source of elementals and not much else. You couldn't actually visit them. A world having that relationship to and that conception of the Elemental Chaos isn't much a stretch. Similarly, the Shadowfell is just a less inhospitable, more developed Plane of Shadow.
And by the same token, the Astral Sea isn't /that/ different from the Astral Plane, it could just be a way of looking at the same ineffable metaphysical layer of existence that connects up the realms of various deities.
For that matter (the different epochs concept), the Lattice of Heaven could have /been/ the Great Wheel - or the Great Wheel could be what's finally re-built in it's place. Or both (making time cyclical). Or the Great Wheel could be the way a prime-material moral philosopher organized the Divine Dominions in a definitive treatise (or the way Sigil's inhabitants choose to). It's not like you could ever actually /see/ the great wheel, nor travel along it from plane to plane as if they were literally adjacent in three-dimensional space.