Oh boy, where do I start.
Commodore's poor code documentation and source control.
The closed mentality of every Amiga owner. I'm not talking about opening up the source, they've always played it extremely close to their chests.
Positioning of the joystick ports, should have been on the side, like the CD32.
Non-upgradeable chip memory. Providing a socket for the chip RAM to go from 2MB to 8MB, or even 4MB would have made a world of difference.
The omission of a pre-amp with volume control and 3.5mm headphone port.
The Akiko chip debacle. And what kind of name is Akiko? It's so not aligned to the custom ship naming convention.
Naming the computers with numbers.
Single IDE header in A1200.