The biggest changes are at the Fjords and Flying Fortresses. The imp-filled road now has goblins, and far fewer than there were imps, and the Flying Fortresses have been completely re-worked. ...
The other changes are that your level makes much less a difference in the damage dealt and taken by enemies of different levels and ranged attacks and spells move slightly slower, enough to reasonably dodge if you pay attention.
Ah, that is probably why I haven't noticed much change as I just started doing Orobas Fjords and haven't touched the fortresses yet. Another good thing to start all over is that I basically knew what lies ahead so I chose battle-mage as a main class, which currently outperforms anything the game throws at me (I rarely even use potions).
First char was warrior and not until later in game I had to be very careful by not getting surrounded, ranged/magic damage was most devastating for me in mid levels. At the end of Ego Draconis I solved this by better level-up distribution and better choices for armor/stuff.
Being unable to dodge arrows before was also a bit annoying as they stung fiercely

The only thing that would probably drive me to go again through everything as a warrior are the new armor/weapons sets. But, I would still like that some kind of a solution is found for the old chars (at least just take the end stats and port it to a new character)