When I do the Pyramid workouts, I do the UB and LB once during the week, and make the third weight workout full body. (and the 4th circuit or full body, if I do 4 that week). I just don't like doing the same workouts over and over again so close together, I get bored.
It sounds like there are some weeks when you DO have time for more than 2 workouts, so you could do GS during those weeks, and Pyramids during the "only 2 workout" weeks. Or you could just do the two upper body GS, and not worry about a leg weight workout that week, since you already work your legs on cardio days with the bike. Or you could add half the GS Legs to each of the two GS upper body days, if you have time for longer workouts on those days. The GS workouts are shorter than most others, so doing 1 1/2 might work. Or, you could do the same idea but do only 2 sets of everything (instead of 3) on the GS upper and lower body portions, to reduce the total time but still get an all-around workout 2x per week.
They are both great, and having some variety may keep you from getting bored, and at the same time challenge your muscles in different ways which probably will help them develop faster (that "muscle confusion" concept).