The actual #1 criteria that almost everyone agrees on is not penetration; but shot placement. For most of this discussion it appears that everyone is assuming that shot placement was adequate. Once you've got adequate shot placement, then you worry about enough penetration to lessen the possibility of defelection, expansion, etc.
The reason I feel that is important is because as others have alluded to, shot placement and caliber are linked. To use just the most basic of example:
If we assume all other costs are equal (a 10mm has the same sevice life and parts replacement as a 9mm), then training ammo costs as of today are:
9mm - $165/1000
.40 - $260/1000
.45 - $300/1000
10mm - $340/1000
So for a $1000 training budget, I can shoot 6,060 rounds of 9mm; 3,840 rounds of .40; 3,333 rounds of .45, or 2,940 rounds of 10mm. Assuming I have an effective training program, which of those is likely to get me the adequate shot placement this discussion is assuming?
Taking your numbers as having face validity (I did not check) you have a point that may or may not apply to individual shooters though will apply to institutional shooters (IE the FBI). The primary limit to what training with a firearm I manage: TIME. I'm not getting to 6,000 rounds a year.
This is why one cannot, IMO, take the FBI conclusion to use the 9MM as an argument that the 9MM is the best choice and apply it necessarily to individual shooters. Chances are the FBI took into account a number of factors that may not apply to a particular individual shooter.
There are a lot of strong arguments for 9MM and many (most) people may find it is the best choice for them individually. The FBI has decided, it appears, that it is the best choice for them as an agency. I still do not get holding the FBI to some gold standard though - they have failed to be ahead of the curve in selecting handguns in ammunition (see the infamous FBI shootout) and, when trying to be ahead of the curve, overshot it in regards to what the agents were comfortable with (see 10MM). Given these blunders of the past I do not see why they are held up as some gold standard.