Many people on here feel the GAP will not catch on, and therefore it will be hard to find ammo for it in the future.
40 S&W has been "proven" in the field, and probably isn't going anywhere anytime soon. It is also cheaper than .45 GAP.
The .45 makes bigger holes and has ballistics similar to .45 ACP. There was a post in the Ammo Can about how the differences between modern self defense loads are almost negligible in all the major calibers (9mm, .40, .357 SIG, and .45 ACP) as far as the proverbial "stopping power" and wound channel characteristics. Hollowpoint expansion is also quite similar.
That being said, I think you'd be more accurate with the .45. For me, .45 is just easier to shoot. Even though the GAP is a higher pressure round, the velocity is very similar to normal .45 ACP. 40 S&W is pretty snappy in comparison, and harder (for me) to make quick follow up shots. I, myself want a GAP, but for the sole reason of just having an XD in .45.
In all practicality, you might be wise to choose .40, just because I don't forsee that cartridge losing popularity, ammo is relatively cheap and easily available. Choose what you think you'll be able to get good with, because if it is one thing I've learned in the forum regarding self defense, shot placement is everything, more important than caliber. And hey, if you're not a good shot, you might like the higher mag capacity of the .40!
-stunks