The Duo-R and RX do not have the CD door lock or ear phone jack + volume dial. They were designed as a sleaker(cheaper) version of the original, like most console revisions.
The regular Duo's have the A/V out on the left side, making it a quarter wider overall and harder to fit in many spaces. The cable's thick long base is also more likely to get stepped on or knocked around on an old Duo. The R/RX's have their A/V in at the center of the back.
The AC adaptor base is partially covered by the top of the Duo R/RX, also making it less likely to be stepped on, ripping it's pcb out of place as I did with my original Turbo Duo.
The Duo R has a CD door eject button the same color as the rest of the shell. The RX has a purple button, the same color as the logo.
The Duo R has it's logo at the bottom middle on the top of the system. The RX's logo is at the top left corner.
Regular PCE/Turbo Duo's are known to have overheating problems and some people offer fan installs because of this. Duo R/RX's are thought to be more reliable and internal fans are not necessary.
The Duo R comes with a 2 button pad physically identical to the Turbo/Duo/SGX/Coregrafx pads. The RX comes with a 6 button pad physically similar/identical to the PC-FX.