Right now, the way secondary suites are assessed for GST purposes, it's not just the construction cost; they incorporate the value of the land. A secondary suite is on land that's already owned by somebody, so in the assessment process they'll include the land to create a value for the property, which obviously—especially in an infill situation in an urban environment where property values are very high—will dramatically increase the taxation on that house, making it very undesirable or expensive.
The result is either not building the suite, or often, building the suite in the underground economy for cash, which is a whole other story unto itself, which is a problem.