First of all such things have been happening since the first items were patented. Such things as the specific motion of a mechanical part have been patented before now. I doubt this will cause stagnation however, it could slow things down. Remember a utility patent only lasts for 20 years and a design patent only lasts for 14 years. In Namcos case taht is most likely a utility patent and will expire 20 years after they filed it. What I think could cause stagnation in game design is everybody using the same concepts. If someone has a patent then someone else has to come up with something better not only to surpass the first idea but to continue to hold gamers attention.

Hi @Ashasekayi!

At first glance, patents on gameplay mechanics might seem a good idea for they enable creators or inventors of these ideas to profit in them. But on the other hand, this might not help those video games enthusiasts to have fun and prevent innovation to occur. One of the issues is that patents are so broad and so prohibitive to fight in court so this very idea of patenting video game mechanics are being shunned away by some companies.
There is also a danger with regards to this kind of patents. For example, Sega owns patent no. 6,200 that entitled "Game display method, moving direction indicating method, game apparatus and drive simulating apparatus." This means that Sega has a lock on the idea of driving around a car around a city with an arrow pointing towards the next destination. This patent was seen on Crazy Taxi.
Just thinking of more patents locking down broad gameplay ideas is quite frightening for it would change the gaming environment.

Source:
http://arstechnica.com/gaming/news/2008/03/patents-on-video-game-mechanics-may-strangle-innovation.ars