1 - The Atari STF(M) 1024 had an external hdd connector, the Amiga should've had that as well, instead of occupying the entire expansion port.
2 - Like the Atari 800xl and most computer-in-keyboard MSX'es, the A500 should've had a second 'expansion port' on the top (and the A2000 in front), to be able to have cartridge games like the Megadrive. Then, games could be much more arcade-like, probably even Neo-Geo like.
3 - Models that came out during/after the A3000 (A600, CDTV, A1200) certainly should've had 31khz video output as a standard option
4 - Since the A3000, HD disk drives should've been standard.
5 - IIRC Commodore delayed for some reason AGA (backwards compatibility issues, rivalling the existing Amiga's too much, that sort of thing). AFAIK it could've been introduced with the A3000 (hence it was slow when it actually was intruduced - outdated)
6 - The CDTV should've physically been an A3000 with CD drive (and with a normal tray, no caddy), and it should've been equipped with a (HD) floppy drive as standard, and the lcd screen should show cd track information. Oh, and it should've been marketed well as a kickass
computer 
7 - I understand that computers 'back in the days' (in the late 80's), were not standardly equipped with hd drives, but surely, games SHOULD have been hd installable (OR should've been on cartridge).