To my knowledge ther is no such program about all you can realy do is to either edit the flight plans on each plane so there is more space, limit the actual number of AI aircraft flight plans or to cut down on the amount of AI traffic.
Spacing has always been a issue even in fs2004 it is not any better.
By far the easiest way to control AI is to cut down the amount of AI traffic. How much to cut it back to will depend on how many AI flight plans you have installed.
The more AI flight plans installed the worse the spacing can become.
Lots of luck 8)