I voted for 9x19mm for a few reasons:
1. IMO, the difference between .45 ACP Ball and 9x19 Ball is overblown.
2. It's smaller, lighter, and has less recoil. The vat majority of people issued handguns don't get sufficient training. While reports of the .45's recoil are often exagerrated, the 9x19's is less, and will let G.I. Joe shoot it better.
3. You can get better penetration against body armor with 9x19, especially with hot loads and/or steel core bullets.
I would like to see a better launch platform, however. The SIG M-11 is fine, but the M-9 should be replaced with the M-11 or even a BHP. The M-9 is ridiculously large for a 9mm and the Walther-style lockup isn't as durable over the long term as a Browning or Petter lockup.