iflyboats,
of COURSE i will cede that correlation does not determine the causative effects of a training stimulus! in years past i have railed against that very type of thinking on letsrun, and i cited the articles not in strict disagreement with you, but more to encourage debate on the topic.
however, there is evidence (again, more anecdotal than emprically tested in controlled conditions) that plyometrics cause an increased return in elastic energy, leading to slight increases in biomechanical efficiency. this is well-documented in jumping and sprinting, as short ground contact times and higher returns on energy are beneficial to performance. if plyometrics lead to similar reductions in ground contact times, much as the correlative studies i noted above, then there is much justification for plyos in training regimen of distance runners. i would venture to say that, based on my experience, they do. i do not claim, however, to have "proof" of this.
as to you second point, again, i agree with the bulk of your claims: some of the work in ex-phys is done without sufficient controls or proper design. however, i ask of you: how do you know these training methods are not valid? how do you know the performance measures are not valid? in many of the studies, performance in time trials is tested...what better criterion than actual time trial results would we need?
finally, i worked briefly in the field. while i concur that there is much to be desired in the standards and applicability of exercise physiology work, i believe that there is much to be learned still from the laboratory work, including in the case of plyometric benefits, just as the labs still have much to learn from the "universal lab" of real-world applications of training in collegiate/professional athletes.