I'd have got rid of the PCMCIA port. It was an expensive (though almost out of date) laptop part. Would have spent the money on A superHD floppy drive, fast RAM and a faster processor. Rejigged the case to allow a 3.5" HDD upgrade, and maybe room for a slimline CD upgrade.
Also, i'd have had the machine boot completely from ROM, with a small amount of EEPROM (upgradable) For wall papers/files/utilities/system upgrades. Maybe 512K. It would then perform a lot like a HDD equipped machine, but at a fraction of the cost. None of that constant swapping disks.
Updated Paula to 16 bit
Maybe add Midi, the ST was on it's last legs, Commodore could have canibalised their market.
Maybe even buy the ROM off Atari and sell Amiga A1200 with ST compatability

Added chunky modes, maybe 24bit modes as well.
Some sort of anti flicker hardware to allow interlace to display better, and be suitable for games.
Maybe added a DSP to help decode audio/video and perhaps help with 3D
Upgraded the blitter to blit 3D objects.
Socketed processor and ram, allowing the trapdoor to be used for other upgrades.
HAM or 24bit chunky workbench. That would have wowed people.
Created a mid range desktop/tower same as above, but with zorro's, but no ISA.
...sold off the pc division early,
...bought some top games companies with the proceeds.