I'll ask someone on our team to give AIR 3.1 a spin, but what I've yet to see is a decently complex Box2D game done with it that runs at 60 FPS and doesn't gobble up memory. Does it play nicely with Alchemy, or would we have to look into using the direct AS3 port of Box2D?
The best example to date is Machinarium, but the fact that it requires an iPad 2 to run doesn't inspire the most confidence in me. It's a gorgeous game with lots of animation, but it's a non-physical game.
Workflow is another concern. If you want to test on the device, how do you do that? Do you have to generate an IPA and sync it, or does it provide some other means to get on the device quickly? This is where generating an Xcode project has a leg up, I think.
Development wise, we actually finished about a month ago, but it's taken a bit longer than expected to get the non-technical parts of this in order. After we launch iStencyl, we'll start off right away on an Android port, which will take a lot less time than this all did.
I havn't used Box2D yet since none of my projects (so far) ever required it. I've seen demos of it (
http://box2dflash.sourceforge.net/) and they perform well according to the info in the top left. I personally use the GPU mode when exporting apps from Flash since that REALLY helps game performance.
To test a game in flash before you export to your phone (Yes, once you export the .ipa you need to transfer it to your phone via iTunes. I just SSH it to my phone and install it to my phone via Installous. I really hate iTunes.), you can easily hit Shift+Enter and it runs the game in a normal window and you can play it normally. Oviously any special things such as use of the gyroscope requires you to test it on the iPhone.
I do my app testing 90% on the computer, and onces it all runs fine on the computer, I just export it on to my phone to do final testing.
EDIT: My first app, Avoid!, uses alot of event listeners which all the adobe pros say you should limit as much as you can. But when the actual game is running, I probably have 40 of them running at the same time and runs fine. I can't wait for the iPad version to be approved in a few days since it's a quick action drag type of game and the bigger screen on the iPad makes it 5x more fun to play. And just for kicks, here's a screenshot of the workspace.
http://i43.tinypic.com/f1fr4l.png (It may seem simple, but each frame on each layer holds a TON of code to make it work properly. And then there's all the MC's that hold even more code).