I personally don't mind so much. I know Pokemon BW, BW2, and even DPP still have an online community behind them, so I suppose that's a bit of a bummer. I can imagine a few other games have something of an online presence behind them too. The 3DS has been out awhile so I suppose it's fair, but they continued to make games for the DS as well during that time. I remember when the Halo 2 servers were taken down. There was a great showing of the community from that.
As for it being wise and sound business decision, I don't know. I know Nintendo has posted an annual operating loss for the past 2 years and is expecting one this year as well, so I suppose I can't fault them.