BryanP -- I went through the same thought process as you a few months ago and ended up getting an A2 fixed carry handle.
Here are my thoughts/reasons:
1. It's classic. You'll see on AR15.com and other sites there are many members who are getting sick and tired of seeing M4'd flattop forgeries with pounds and pounds of equipment hanging off the ends -- for what? These guys aren't even in the military and they're attaching $350 Surefire lights, IR devices, forward grips, RAS, etc. What you end up with is a self defense carbine that weighs more than an M1A. I think folks who get an AR flattop figure they NEED to add all this stuff to it, since it's a flattop.
2. What's the purpose of your rifle? Mine is for self defense and plinking under 140 yards or so. Why 140 yards? Because that's the lethality limit (i.e. tumbling limit) of the 5.56 M193 cartridge out of my 16" M4 profile barrel. I don't plan on shooting my AR at 200 or 300 yards, and I don't varmint hunt. If you do plan on doing either of those things, then get the flattop -- it makes mouting a scope easier.
3. You can easily mount optics on an A2 rifle -- just look at the newspapers for photos from Iraq. Plenty of folks mount their optics -- I'm talking about red dot sights, EOTECHs, etc. -- atop the carry handle, or cowitnessed with the iron sights in front of the carry handle, above the handguards. ARMS and others make mounts for this (the forward mounting option uses what some call a "gooseneck" mount.) Mouting atop the carry handle doesn't require too funky a cheek weld, plus you can get a "Delta" style cheekpiece if you want (about $70). It's also gives you a nice, erect "heads up" style of sighting that I believe gives you more situational awareness and peripheral vision in self-defense scenarios, though others will tell you it places you head too high and makes it too easy a target, which is a criticism of the M16 A2 sight style anyway (at least to some). But the A2 sight works great for police and military wearing helmets and gas gear.
4. The A2 sight IS tougher becasue it's integral to the receiver. No one can tell me that a thumb screwed anything is tougher than seamless aircraft grade aluminum. This was one of my main concerns, especially in a self-defense scenario. What if I drop the rifle? Bump it on a wall? It slides down the stairs with me? I have to whack someone with it, then sight and fire at a target some yards away? Is a screw-on A3 going to survive that? I bet the answer is 99.9 percent yes. Do you like 99.9 percent odds? What if you have taken the A3 off and just mounted a red dot or a low magnification sight there? Will that survive? On an A2, you can have a sight mounted up top or in front, and if it's ever knocked off, the battery dies, or it is knocked out of alignment, you still have the irons.
5. YES, you can and should buy back up irons for an A3. have you ever priced them? If you think an A3 sighted AR is $80 to $100 more than an A2, try adding the price of a rear flip-up sight and/or a front/rear combo. Ouch.
6. Want to go with a short barrel/A2 fixed sight, and a longer barrel/A3 flattop for possible precision shooting in the future? That's one of the beautys of the AR system -- Just buy another upper receiver! You can even buy it in another caliber!
To sum it all up, what is the purpose of your rifle? Self defense? I'd go with an A2. Plinking? I'd go with an A2 with a red dot sight. Varmints? A3. Targets? A3.