As far as marketing strategies go, the Pokemon Global Link (and subsequently, Dream World) was shut down to promote the Gen VI games. By removing one of the features from Gen V, it influences people to go buy the newer games, giving Nintendo more revenue. It also let them reintroduce GL in Gen VI with a better system.
It's also true that the amount of people playing Gen V will drop anyway, and maintaining both systems would cost more - however in retrospect, the cost would be minimal to a company worth nearly 20 Billion USD.
