Last year, if I remember correctly, Apple had only the deliver to home option. The in-store pickup was an option for iPad pre-orders (the one I went with) but I don't think it was available for the 3GS.
Even if it is offered this time round, I'll stick with my local AT&T guys (if all is the same as last year) because it will be easier with phone number swapping and activation etc I think – we'll do another hand-me down scenarion with my wife taking my 3GS etc.

I appreciate your insight. So, if I understand correctly (based on last year's experience).

Pre-ordering via AT&T requires physically being in the store, but Apple allows either in-store or online?

This is going to be fun! First purchase will be iMovie.

The details may vary a little each year, so it's best to speak directly to someone or check web site details for both Apple and AT&T pre-ordering options.
I can say that last year I opted for pre-ordering via AT&T – mainly because I know my two local Apple stores always have sizable lines on iPhone release days, and Apple's pre-order system is via home delivery and I just don't 100% trust their carriers to deliver on time. I've heard too many launch day stories of shipping being delayed by several days at the last minute.
With AT&T last year, we went on the first day pre-orders were possible and reserved the new 3GS for delivery to our local AT&T store 5 minutes from home. Went in the store, made our pre-order, it arrived for launch day, and they dealt with pre-order people first on launch day. We were in and out in around 45 minutes even with activating new 3GS, swapping my 3G to my wife and moving her number from a 1st gen iPhone to the 3G and shutting off phone service on the V1.
All round dealing with AT&T – at least here in Austin at our local store – was great.

I wandered into the store last year and got the very last one with no wait. No one believes me, but it was really that smooth.

Apple Store is a 45-minute drive each way, so I'd prefer to receive it by mail, but not if I get it later. Also, will the Apple Stores be so packed, that it will take forever to get one activated (even if I prepay/order)? Can I prepay and pick it up at the AT&T store?

They are making a generous offer for me family. I signed a legal contract that committed me to 2 years. After 1 year, they will allow me to restart that (i.e., save a year) and give me brand new customer pricing again, only a year later. Note: I don't love AT&T and they are doing this to lock us iPhone users (very profitable to them) down because they see a real threat on the horizon, but I do love their handling of this. If I bought the Spring Palm Pre there is no way I'd get new customer pricing on the EVO.

I completely disagree.

I got my 3GS on launch and will get this on launch too.

Its going to be faster (which is good since iOS4 introduces multitasking, and the new apps will push this further and further, especially things like iMovie. Games will be more precise (the Gyroscope). My wife and I take 90% of the pictures and videos of our toddler with our phones. Knowing those videos will be in HD really matters, and being able to take them in less than optimal lighting conditions is worth the upgrade to me alone. The front facing camera is only a gimmick when its stuck on iPhone4 to iPhone4 wifi only, when that changes it will be terrific. The battery life is an important upgrade. Better call quality is presumed since the new antenna and addition of another mic and noise cancellation.

So to review:

It does everything my 3Gs does
Everything I do will look better
Everything I do will be faster
Better photos better videos (and the iMovie is going to be terrific), probably better optical recognition implementation
Better gaming experience
Longer lasting battery life
Thinner, more comfortable profile

This is exactly WHY I upgrade. To enjoy my experience even more, and to gain new features that add to my experience.

Let's wait in the near future

That said, if I were to get a new phone, I'd probably go get a Sprint Evo; but I won't since a jailbroken 3GS will more than suffice for another year.