Well, let me be the Devil's advocate here. One of the things that makes scouting hard in baseball is that measurable skills often have little to do with success in baseball.
With the Red Sox, we never had any player who had measurable skills the same as Wily Mo Pena. Wily Mo was huge, all muscle, fantastically strong, could run extremely well, and could throw a baseball 100 miles an hour. But he couldn't play baseball.
In 2006 we traded Bronson Arroyo for Wily Mo. . ..an awful trade in retrospect. It was a scout's trade. Our scouts loved Wily Mo; ALL scouts loved Wily Mo. I just saw Bronson being interviewed on NESN, and he talked about this exact point, not referencing Wily Mo but his own career. He had a long career, won 150 games or something. His explanation (paraphrasing) was, "it's become a max-effort game. Everybody thinks that you have to pump up and throw 100. But it is harder to throw strikes, and it puts strain on your body, and after a couple of years you have to have surgery. I just did what my body was able to do, pitch at the speed that I could sustain. That's what you do to have a long career."
Bronson was the opposite of Wily Mo, a guy WITHOUT apparent ability, but who could play baseball.
Suppose that you segment "athletes" and "just baseball players" into ten levels. If you have a bunch of Level-10 athletes with a Level-1 understanding of what Bronson was saying against a bunch of Level-1 athleetes with a Level-10 understanding, then obviously the Level-10 athletes will win. A team of short, fat guys is not going to beat a team of Wily Mo Penas, no matter what.
But suppose that you have a team of Level-10 athletes with Level-8 understanding against a team of Level-8 athletes with Level-10 understanding. I would bet that the Level-8 athletes would crush them, over the course of a season.
It seems to me that your point SEEMS true, looks true, because we think of athleticism on a scale that is relevant to ourselves. Obviously, an athlete competing with someone like myself in any athletic endeavor, the athlete will win. But if you start with 1,000 guys and take the 50 best athletes in the 1,000, it's a different thing.
I'm not convinced that incremental gains in running speed or fastball velocity are going to lead to higher quality of competition, IF THEY ARE OPPOSED by backward steps in gut-level understanding of the game.
The steroid era proves that gains in STRENGTH are certainly meaningful, among people who can play baseball anyway.
I'm kind of losing my point here. Dustin Pedroia was never an elite athlete, in a certain sense. He was small, not particularly fast, didn't have a great arm. He was the opposite of Wily Mo. But he was smart, super-competitive, had great wrists, and he was willing to pay the price day in and day out. One Dustin Pedroia is worth 100 Wily Mos. I'm not sure you're going to be able to measure that. It's nearly impossible to measure that on the level of the individual player. To measure it on the level of the game as a whole would be another level of complexity beyond that.