Measure current for Field Oriented Control
Both methods have advantages and disadvantages. In method 1 you don't need any serious bandwidth, just about 100kHz is enough. Also you get isolated measurement, which is very good. Just remember you can also sample the third phase to detect short circuit. In method 2 you don't get good short circuit protection, your bandwidth should be at least around 2MHz, since current doesn't always appear on shunt resistors, you don't get isolation for free, but you can use cheap and simple components. 

So in the end it's your call, depending on application. I used both methods and can't say any of them is always better than the other.