Glocks are great. I'd take one in a pinch any day.
Given the OP's situation I still would have opted for the M&PFS9. I would prefer to have the better sights and longer sight radius of the Pro, especially for three gun. And, the FS9 is a great carry gun(especially with Trijicon HDs) on the same platform as the comp gun. Plus, I shoot the M&Ps about 8% better(faster and more accurate for me, I've run the scores).
But, nothing is wrong with a Glock17(I ran one for several months this spring) that can't be fixed, and I know tons of great shooters that run them.
I think the OP will ultimately sell one or the other and concentrate on one platform, only because that is what I did, it makes life simple.
OP--I have two G17 mags with Dawson six round tuned extentions(23rnds) that I would be happy to sell if you want them, they are the bomb for 3Gun....