PNG Icons have these advantages, at least:
* They're flexible and expandable. The PNG format can support lots of nice tricks.
* They can support up to 32 bit colour (24 bit with alpha channel).
* They are supported by other platforms, including Linux. Just pick up files from there, no conversion.
* They are proper chunky data and not hacked.
The native Amiga icon system can't do any of these things, and that's just things I can remember.