I actually asked this question recently to Adams driveshaft and they said that they felt that the flange was stronger and was what they recommend due to a larger surface area.
Definatly the flange. The yoke with straps that are little more than sheet metal and the tiny bolts are the last choice. A yoke with u-bolt is considerably stronger than the strap type and will suffice in most any application. If you already have the u-bolt type I dont believe it is worth the trouble to convert to a flange type.
I would say a yoke is going to be way stronger. Most flanges only come as cast parts were as you can get u-bolt yokes that are forged. Look at almost every Ultra4 car/Rock buggy or even drag cars. They almost all use 1350/1410 or even 1480 U-bolt yokes. If flanges were stronger all the top guys in the industry would be using them. Also some flange combos are longer then a standard yoke. In some applications an inch in driveline length can mean getting a full 14" of wheel travel or having to strap your wheel travel at 13".