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The 2016 cars are actually a lot faster. 2008 was a wet year, but we can use 2009 as a measurement, Suzuka in particular. For GT500 a 1:55.394 was the fastest from any session for qualifying: http://supergt.net/archive/classic/supergt.net/supergt/2009/0906/0906qual.htm
GT500 pole in 2016 was a 1:47.456: https://supergt.net/results/index/2016/Round6/3/gt500 (middle of the three tabs above the results)
Note that GT300 was only just over 2s off the 2009 overall GT500 fastest lap, plus the 2016 qualifying lap was a whopping 10s quicker than in 2009!
A lot of speed differences comes from the advancement in tire technology and compounds.
Tires have improved a lot in the last decade and can be a POSSIBLE reason for such a difference in lap times. This goes for all motorsport racing.
Not saying this is the case here but very possibly a major part of the differences.