If I were to decide changes for the AGA chipset, I would have added a chunky 8-bit graphics mode like VGA mode 13h and tile/layer based modes like for video game consoles. I would also have wished for more sprites or a faster blitter, and an additional soundchip like OPL or any OPx for music and general MIDI compatability. In 1992 this would have given it an edge over PCs I think.
Of course, I don't know much about time/price constraints at the time, and I know little about the Amiga hardware design to be able to tell if such changes would be possible while retaining backwards compatibility.