I addressed all of these in my post, but I'll elaborate:
[*]Less secure than either messenger bag or backpack.
Secure meaning stability? I've used panniers since the 80s and never ever ever had one fall off. These days I use Arkel and Ortlieb panniers... both types attach and remove easily and quickly... and stay attached to the rack even when I'm traveling at fast speeds on chunky gravel or bumpy trails. Yes I've heard of panniers falling off, but I think the problem was either cheap panniers, user error, or both. The Arkels and Ortliebs are pretty foolproof though... you don't need to pay attention to what you're doing. They are simply quick, easy, and reliably secure.
[*]Hassle if you have to stop to go in a store -- do you leave it there and risk it being stolen, or carry it with you? In which case, you've got the hassle of taking it off and the hassle of carrying an awkward burden.
I mention in my original post that this is one of the advantages of messenger bags and backpacks... if you make frequent stops you have nothing to take off the bike. However, if you use a backpack you will need to take the backpack off so you can get to your lock, lock up the bike, and put the backpack on again. In my experience it's just as quick to remove a pannier. Messenger bags are the speed winners here though... just unbuckle, swing around, and open the flap. Still... not like taking off a pannier takes more than two seconds... unless you have panniers with a bad mounting system. Good ones go on just as quickly.
[*]Hassle if you need to take your bike up a passenger elevator (which almost always means vertically).
Really? Have you ever done this yourself? I have... many times. I used to take my bike on the DC Metro, which requires long elevator rides to the underground. I never noticed this being any more difficult with panniers than without. If your panniers are on the front it might be another story, but how many people commute with front panniers? The front end of my commuter weighs the same whether I'm carrying a pannier (or two) on the back or not. I simply lift the handlebars until the bike is vertical, and hold the rear brake to keep the bike from moving if I need to. If anything a bulky backpack can be more annoying in a crowded elevator because you, your bike, and your backpack take up more room than just you and your bike (with panniers attached) would.
As I mentioned in my original post, there are advantages to messenger bags and backpacks sometimes. Messenger bags are absolutely the best when you need to get in and out of your bag quickly. Handlebar bags are also great for this, but messenger bags hold a lot more. Also, if you need to lift or carry your bike a lot, a messenger or backpack will make this easier.
I also feel a bit better about carrying an expensive camera or laptop in a messenger bag or backpack. The contents of a pannier may be subjected to more bumps and vibrations. Maybe not enough to do any damage, but I just feel better keeping the camera on my back (even though that's probably the worst place for it if I have an accident). That said I've carried my camera and laptop in a pannier many times. Not something I worry about for road riding, but off-road is where I feel better keeping it on my back.
Sean