Its probably a bit impractical, but what about having the start of the main runner the same size as the turbo exhaust port and have it tapering up to the right size to mate with the rest of the exhaust (2.5" usually?). This should give a smooth flow as the exhaust gas doesn't get a chance to suddenly expand and slow down because there's no sudden change in pipe size. The wastegate pipe can feed in wherever's easiest as the pipe diameter is always bigger than the turbo port.
Feel free to tell me if I'm talking a$$,