Lots of great ideas already. Especially increasing the Chip Ram and having all major chips be socketed. Oh and they should have done away with this 15khz nonsense after the A3000. Built in accelerated graphics too ala CyberGrafx/Picasso or maybe a compatible AAA design. 16-bit sound as standard and call her Super Paula.
I'd also make the case larger and a bit less cramped. Should have more personality to it than the A4000 box. Something alone the lines of the A3000, but maybe with standardized 3-1/2" HD floppy drives and a slim line CD-ROM, like what the laptops had.
Speaking of laptops, I would have done away with the form factor of the A1200 altogether and gone with something more along the lines of the A600. This machine could be 100% surface mounted, unlike its big box cousin. And I'd design it so that the customer would have the option to turn his new Amiga into a portable by adding a battery and a screen that you'd simply thumb-screw into place on the back of the machine. If the battery technology still sucked and you couldn't add something internally, then a real thin, but large footprint designed battery that mounted underneath (raising the machine a bit too for typing) would have been implemented.
So yeah, I'd have a mid to hi-end "workstation" type big box and a semi-portable, which was what the A500/A600/A1200 kind of where or could have been. If someone wanted a nicer keyboard for their new portable - there'd be a port so you could hook a regular/large big box styled keyboard to it.
Both machines would feature the 060 (cost would be driven down thanks to aggressive negotiations), a true accelerated graphics chipset, 16-bit sound and HD floppies. Finally, I'd market the hell out of the machines in professional circles as what they were 'and could be' instead of narrowly focusing on a particular market like they did so often with graphic artists or other "creative" types.
Cut deals with schools on the hardware and make up for it in licensing and software. 'Power Up' programs for consumers would be mailed out to each and every Commodore owner and speaking of lists/serial numbers - I'd have maintained a much better relationship with previous Commie owners all this time. Newsletters with constructive input forms for sure instead of paying some company to tell us who are customers are. lol