With GMAW there is a *large* risk of Lack-of-Fusion between the weld beads. Thus IMHO, SMAW is the best choice of the two. Other good choices are GTAW, and on larger flanges FCAW.
Weld size is per Code, so what Code are you using? Typically, the throat of the fillet has to equal or exceed the wall thickness of the pipe, making the filletweld leg size 1.4 times wall thickness [square root of 2; 45° right triangle]. Thus the amount of weld on a heavy-wall flange is huge; 3/4" minimum on an 8"NPS Sch80/XS pipe. Thus the preference for weld-neck flanges.