SCT is more complex, so if you are doing it yourself, its a steeper learning curve, with less available information/support.
But it is a flash solution.... no wiring, and access to way more paramaters than Vec.
In the end, both can modify timing and fuel, so they will make the same power.
If I was doing a more serious build (big boost), I would definitely go stand alone. But for the typical street build, the SCT will do more than you need, and it can handle boost, however, it is not inherently built to handle boost, so some creativity is required.