A couple of thoughts:
1. The baseball analogy is a poor one at best. The long-term health of baseball is about old, fat people WATCHING professional baseball, not PLAYING baseball. The long-term health of golf is based NOT on watching the PGA Tour, but the same old, fat people that watch MLB PLAYING golf! That brings a whole complex of variables into play in golf that just don't exist in baseball. That's why a competition ball/bifurcation in golf is a vastly more complex and nuanced situation than the wood/aluminum bat issue.
2. If the PGA Tour has a problem, why don't they address it? Why put that at the feet of the USGA entirely? The USGA is such a convenient whipping boy in all of this, but the reality is that the Men's U.S. Open is the only USGA event in which there is a possible problem with distance.
3. The current ProVI generation of balls is still, even at 120 mph swing speeds, well within the ODS parameters that were in place and totally non-controversial for years. RIGHT NOW, THE PROVI IS FAR FROM THE LONGEST BALL OUT THERE! So again, it is a Tour problem.
4. Granted, the USGA testing methods didn't keep pace with equipment changes, but how could they? There was a "perfect storm" situation here; a booming economy, a booming golf industry, and booming availablity of new materials like urethanes and titanium. The rule in technology advances is that they accelerate geometrically as one development leads to another. It is really easy to look back now and say that it should have been done differently, but who among us saw the complete future in the late 90's?