Sure, for example there are other collision methods, other buffering methods (Unreal uses Portals, BSP and so on...), other engines... 3D isn't = 3D, some engines just show the game from above (as GTA), other are 1st person as Unreal, sometimes you see the player (Tomb Raider) or there are not really 3D worlds (Jump 'n' Runs as Pandemonium or Goemon64...) or you need to see a big landscape (Black & White). Also the collisions and stuff, maybe you need to deform the map or just move objects around. And the physics engine, you don't always need gravitation...
There are many differences