It's something more fundamental. When writing software for mobile devices, you really need to optimize for power consumption. There was a recent talk at Google IO about the new polling vs pushing for web services, and it's alarming. If your Android app polls a web service every 5 minutes, it'll use something like 10% of the battery in one day (just that one app!).
Flash apps are simply not designed for optimal power consumption. Flash is designed for multimedia apps, which are generally power hogs.
I develop Flash professionally, and I'd never run it on my phone.
I'm mostly worried about Flash in the context of network usage. I can't say how the power performance is for graphics and gaming, but I'd guess it's about the same as native phone apps.
It's easy to imagine flash apps with network access patterns that aren't optimized for phones. Take any advertisement or analytics system which continually polls the server for more data. This will kill your battery if left running.