Time for a daydream! What if you could combine elements from different old computers? And what is all those elements worked perfect together? What kind of f*cked up Frankenstein would you get? This is my result:

Sound: 100% SoundBlaster comparbility, dual SID-chip, build in MT32 and MIDI connections
Graphics: Build on Amiga graphics
Support for: Floppy disk (5 1/4 and 3 1/2, all sizes), CD, Harddisk, USB
OS and software: Support for wide range of old OS'es (alternatively special editions of old OSes), including MS-DOS. Support for multi-OS. Hardware drivers would be needed, so you wont exclude possibilities the hardware could give you. No emulation needed.
Additional: Even if this would be an entire new system based on old ideas and hardware, it is important that the feel and results of the machine is as authentic to the original as possible. Flexibility of the system is also important.