Device upgrades are fairly rare for most users, as is wiping the cache. Upgrades tend to also happen when plugged in, allowing the AOT compiler to run the CPU at full speed without impacting battery life.

Also consider it may not just be the one app the user launched that needs to go through the JIT compiler. With intents as Android calls them, an app may be calling functionality from other apps on the system. Each of those other apps is also going to need to go through the JIT compiler. I'm unclear when the second JIT run would happen; at initial app launch, or when the user taps a share button or similar action that invokes the second app. I'd hope this happens all at initial app launch, to avoid a random performance hitch after tapping a button.

I can see where this is going to slow down some development or those users who frequently upgrade their phone with community builds of the OS. It seems this is mostly a decision to benefit the majority of Android users who don't develop for their phone or root it. They are going to tap upgrade for their OS every once in a while and have a longer process. In return when they tap Angry Birds, it's going to launch a bit faster and save a bit of battery life.