The A600 has crappy smd capacitors which are leaking and wrecking boards as we speak.
The A500 is more desirable in that aspect (providing the barrel battery has been removed before motherboard damage).
You can't have a DMA connected hard disk on the A600. So another feather in the A500's cap.
I read somewhere though that you can't have graffiti emulation for Doom on the A500 with the IndivisionECS. Maybe I'm wrong... Can anyone clear this up?
Size, well if size doesn't matter then it makes no odds. I prefer the A600 size wise. If you want an 80's feel, then go for the A500.