For an execution, where the subject knows for certain that he's going to stay on that cross until he's dead, I think that nails are the only way to go. We'd lose too much by giving up the steady deliberate nailing—one nail at a time, with brief pauses between nails so that the subject can experience the pain of the nails that've been driven thus far, and anticipate the ones yet to come—and so that the subjects who haven't yet been crucified can see what's soon to happen to them.
Moreover, using nails through the ankles allows us to crucify the subject with the knees extended: he can lock his knees and support himself with his legs, but only at the cost of putting his weight on those nails. In the initial stages of the dance, he tries to relieve the pain in the wrists by straightening his knees, but almost instantly feels the burst of agony in the ankles and drops back down.
Some time ago, Jerkbot posted a rendering that included a hybrid: roped wrists, nailed ankles. No complaints, but I'd have preferred nails.
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The only time I'd really favor the use of ropes is when the subject is allowed to believe that he might survive. POW's
"Double Cross" is a terrific account of an endurance contest in which two young men are crucified with ropes, with death on the cross the penalty for the loser. There're some problems with the mechanisms described in the story, but the writing's superb, and it's a must-read for male-crucifixion enthusiasts.