D3 minuses:
No battles on the ships, no creatures in the water, no city sieges with warmachines, no more resources (wood, iron ...), the guardians without summoned animals, the campaign videos only with flying artworks, no underground maps, no arenas with various elevations and shapes, only 3 races, very few neutral units...

D3 pluses:

3D graphic, the movement and spells at the arenas, the runes, the skill system, the possibility to modify thieves and land guardians, arenas with bonus boxes and barriers, various weather and day phases, the respawn in neutral buildings, 3 sets of armour and more parameters for heroes, the special abilities, the cover points, the capital stores, the underground arenas, the new story, the new heroes.