Personally, if I were looking at a Glock, I would go with a 9mm, just because I have a personal preference for a fully supported chamber, and in a Glock, you can only get that in 9mm.
Not that there is anything wrong with the 40 or 357 rounds, or Glock pistols chambered for them. I only prefer the 9mm (in Glocks at least) for my own peace of mind. Besides, with modern bullets, the 9mm is no slouch for personal defense, plus ammo is still cheapest in 9mm, and nines are more fun to shoot, for me.
That said, the only auto I currently own is a 40 (a Steyr, with traditional rifling and a fully supported chamber), and I carry a Beretta 96 daily at work. However, my next centerfire pistol will either be a Glock 17C, or a 1911 in 9mm, and I would not feel handicapped in the least if my agency issued a 9mm pistol instead of the 40.
Best of luck with the decision before you.