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I agree with Mike W.'s implied criticism. Some sort of systematic error (or just "difference") in the measuring apparatus would show exactly the same change. Maybe you have complete confidence in pitchFX data, but the average reader doesn't know enough to. Could readings be different at different stadiums, or on different days? Is there a calibration process? How, if you think about it, would you produce a "standard" 90mph fastball, to be sure your setup was calibrated right?
I know this is just a quick post rather than an article, but if you had a link to an article that covered the reliability of pitchFX it would have been useful to put it in.
And as for strongarming Excel into plotting several sets of data points on a scatterplot, davelew had that right - at the "source data" step, click on "series" and use that window to make sure you plot "game 1 fastballs vs. pitch count" and "game 2 fastballs vs. pitch count." You'll figure it out - you enter the x and Y ranges separately for each "series" (game in your example). Excel sucks for scatterplots but you *can* bend it to your will this way.