Indeed. These wonderful little mikes and modern software/soundcards enable the amateur to quickly acquire mountains of useless and invalid data. Anyone wanting to get good results will need to do some studying, and you can't do any better than Joe d'Appolito's "Testing Loudspeakers."
Until you understand the concepts of sampling, resolution, windowing (apodization), near field, phase unwrapping, truncation, time vs. frequency, and gating, what you're going to end up with is a bunch of messy curves that tell you more about your measurement errors than about the loudspeakers.
Here's link that will give you a flavor of a few of the issues, but really, if you want to do something useful, you need to go into much more depth and practice. http://www.bksv.com/doc/bo0102.pdf
Good article, I used to use a very expensive B&K test system for telephone handset measurement.
The WM61A is a pretty flat device, but works best if it is mounted on a wand of the same diameter and long enough to reduce reflections from the stand.