The heavier bullets penetrate deeper in living soft things. Which to me is a huge advantage; and I'd put money down on the base that whichever caliber/load does more "damage" to the gel block indeed creates a bigger/more fatal would channel.
I have to disagree with you here. There are loadings in all the calibers that meet the FBI/IWBA standards for penetration.
http://www.ar15.com/ammo/project/Self_Defense_Ammo_FAQ/MiscDocuments/HandgunBulletchartaspicturerev3.jpg
For that matter there are 9mm loadings that penetrate more than 40SW and 45ACp, and vice versa. Penetration isn't just a matter of bullet weight and diameter. Saying heavier bullets are a "huge" advantage, is frankly exaggeration imo. We're not talking 5.56 vs. 7.62. The differences in velocity and mass aren't nearly as dramatic. For that matter, excessive penetration isn't desirable either.
And again, this idea of the fatal wound channel is to me overblown. Handguns stink. You need to penetrate to the vital organ or central nervous system and have enough mass to disable either of those in order to truly end a fight with any speed (and the less time the adversary has to shoot at you the better). Having that adversary bleed out slowly over time is not the goal.
I'm sure you know the Miami FBI shootout, which rather famously lead to the development of the 10mm and then the 40SW. What you might not remember was one of the bank robbers (Platt) his lung had 1.3 liters of blood in it when the autopsy was done. The man would have bled to death had he escaped that fatal wound, which was, wait for it, to his spinal chord. Yet during that fight despite bleeding profusely internally and having been shot twelve, that's 12, times he continued to fight and his actions killed two FBI agents and seriously wounded 3 others.
Now you can look at this as, "Well that's just cause of the puny 9mm!" and yes the 9mm loadings of the time weren't particularly good. But look at the ballistics tests that I linked to in terms of depth penetrated and expanded diameter (and every self defense ammunition manufacturer has similar charts available on their own websites if you dig around). The differences aren't huge, they're just not.
The idea that a more powerful handgun caliber was the solution to all this has been fairly accepted today by most instructors for private and law enforcement purposes as an attempt to avoid blaming the dead agents. Engaging well trained adversaries with a semiautomatic rifle and a shotgun when all you have are pistols and two men with shotguns is why that fight went that way (and the agents chose to stop that vehicle at that time, they weren't forced into the situation and there were other agents with submachineguns and rifles working the area). Don't bring a pistol to a rifle fight, because again handguns stink. Unless you have a shot such as in that fight that damaged the central nervous system or a major organ that causes a rapid bleed out, you're just putting holes in a person that might stay up a long time. And I think at this point ballistics tests show that any of the major calibers can penetrate to the required depth to make those critically damaging shots.
Obviously you prefer 9mm and that is fine but to state it does more damage in any loading is just false.
People get hung up on this idea. That because the 40SW penetrates maybe somewhat more or expands maybe somewhat more (and again, different loadings have different results) that it's undeniably better. The debate here is really whether that difference in "power" translates to a real world gain in terminal effect, and I honestly can't see how that difference is argued to be significant with the testing done in recent years. Does that mean I think 40SW stinks? No. I've seen its effect on auto glass and certain barriers first hand and I can see why people might to go that route. But against a human body I think saying any difference among the primary handgun calibers is "huge" can't be backed up.