Permit me to turn this around. What advantage (aside from the tired tale of mag capacity) does the 9 offer over the .45? (Please don't bring up recoil or double taps because I can load a .45 with half the recoil of any OTC 9.)
What load would that be for .45? Do you lose the advantage of a heavy bullet by making that load? How's the energy? Power factor? Reduced recoil with retail ammunition (not everyone loads their own, ya know) is a completely valid reason. You can't really argue advantages/disadvantages against personal preferences - the whole apples and oranges thing.
Ammunition that's half price and allows for more range time (which is why I chose it) is another good reason. Capacity is also an advantage, or at least a trade, as has been mentioned.
Round-for-round, what about the 9mm is better than the .45?
If an individual could equally afford each, and shoot each equally well, .45 would be better because of the larger round advantage. However, that's a very idealistic comparison. 9mm platforms are typically very different from .45 platforms, the recoil of each is different (I won't even say one is more or less, but they're very different feeling), ammunition selection and costs are different, etc. The ultimate criteria is "Can the user quickly put that round where he/she wants it to go?" There may be a dozen reasons why the shooter could shoot 9mm better than .45, or vice-versa, so round for round, if the shooter is willing to trust both, it comes down to preference.
If the shooter is competent, it's more than adequate. Just because there's better than the 9mm out there doesn't mean 9mm is bad.