When a developer makes the same game for multiple consoles at the same time these are called ports. Most of the time ports try to be identical to each other. Not only is this much easier on the developer but the public tends to prefer the idea that the game they are getting on their console is just as good as the game on their friend's console. However, no matter how similiar the games are it is impossible to expect that the games will be identical. Every console has different capabilites and hardware and it is impossible to perfectly emulate the experience across a wide range of consoles.
As I stated in my previous blogs about controllers (part 1, part 2, and part 3) every system has their own unique control scheme and every single one of them can change the way their games are played. Currently the Xbox 360 and the Playstation 3 are the closest in graphical capability so many games do cross over. The PS3 controller has motion control built into it, while the 360 does not. This leads to some developers adding some extra gameplay mechanics that use the motion controls of the PS3.
One of the unique examples of the Wii game being better than the 360 counterpart was "Ray-Man Raving Rabbits." The game was originally designed for the Wii and had a great deal of motion control used in a fun way. The 360 had no motion controls and most of the fun and charm was lost on the port. The 360 tried some things using its camera but it was mostly an afterthought and not fully realized. Wii reviews, 360 reviews.