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With Star Raiders, for instance, the joystick is necessary to enjoy the same experience as an original user. Arguably the boot up sequence too and the CRT monitor.
Another example: "Daredevil Dennis" on the BBC Micro. The internal speaker on the system produces the sounds. Good luck reproducing that efficiently. And just the reality of sitting in front of the machine itself, loading the program from 5.25" disk and using the original keyboard to play the game completely alters the whole thing.
- not to mention the fact that an emulation of the hardware is going to be imperfect.