The problem, though, is not with how peremptory challenges are conducted, managed, or whatever. It is with allowing peremptory challenges at all. They are almost always used based on stereotypes at best: "That well-educated male middle manager is very likely to be a law-and-order type, so the prosecution wants to keep him and the defense wants to get rid of him… except in a white-collar-crime trial, when it's probably the reverse." It makes much more sense to slightly lower the standard for challenges for cause, force a complete record to be made of that challenge, allow the challenge for cause, and get rid of peremptory challenges.
Admittedly, some of this comes from my own experience in the military. I was called to serve on 40-odd military courts-martial and administrative discharge boards (about two-thirds of them courts); I was peremptorily challenged off of 32 of them because, at that time, I was a sitting commanding officer. Among military defense attorneys, there's a bit of received wisdom that commanding officers believe other commanding officers' accusations and convict more often on dubious charges, and are virtually certain to vote for more-severe punishment, than do other officers. I think that would have been untrue of me; but, in any event, it quite possibly hurt two defendants because the single peremptory challenge was not available for use against other officers not as willing to listen to the evidence as I was.
More later today on Merck, after I finish digesting it. I think I'll need something to deal with stomach acid, though; perhaps I can find an alternative that isn't in patent…
Update, 1115: You can find PDFs of today's opinions on peremptory challenges here: Miller-El (reversing the Fifth Circuit) and Johnson v. California (reversing the California courts on the standard of inquiry). After quickly reading both opinions, it seems to me even more apparent that what the prosecutors wanted was a jury in their favor, not a jury that would do justice. That alone is reason enough to me to peremptorily strike peremptory strikes: that it has taken a quarter of a century for Miller-El to get even the semblance of a fair trial.