Eeh... I'm with buttrump. I think this topic is probably best discussed over libations as I really don't have passionate opinions about it. FYI, I didn't search the publications to make an argument one way or another. Those were just the publications I could find on the subject.
Warily...
1) The reduction in muscle use could correspond to an increase in efficiency - with a clipless pedal less muscle is not engaged in the action of keeping the foot positioned correctly. Even with a toe clip you have to exert some effort to keep your foot positioned correctly. It's similar to the increased ability to lift weight on a universal or guided weight system over free weights - guiding the weight - guiding the force of your pedal - is expensive in terms of energy.
So more muscle groups, yeah? That's probably why lifters like working with free weights. I would buy the efficiency argument, except the research seems to counter that (see previous posts). Other posters pointed out it's more for power than for efficiency (which I'm willing to believe).
2) The correct POV on clipless is that they allow you to get more muscle groups involved in the production of power. The key element is that they don't just enable you to get more muscle groups involved, that paper questions that, but that they allow you to get more muscle involved in moving you forward. You can get all your muscle groups involved by flailing around with some hand weights and ensuring a brake pad is rubbing, but you won't move forward very fast. Clipless get the power going in the right direction.
Okay, so you can push harder, but you're not "pulling." This is what the Rivendell hi/yu-ppies were saying.
3) Clipless are a ton safer than toe clips. You can clip out in any position at any time, and you can clip out both ways. Because the clip out is a twist, when you go down they tend to prevent the worst orthopedic injuries - twisting of knees or ankle which damages ligaments. Twisting your leg in toe clips will not let you out, and it's very easy to destroy your knee by going down awkwardly in tight toe clips, or even loose ones.
I don't have any numbers on what injury rates due to pedal interfaces. But I do hear about stories of people tipping over while clipped in, and at least some of them have resulted in broken bits. Actually, I've seen somebody tip over.
"This will not stand. This will not stand, this aggression, uh, against clipless."
