In my own experience, I have found the original CD-ROM systems (PC Engine *and* TurboGrafx) to be freaking bulletproof, even under heavy use/abuse. I've owned a handful of each over the years and the only problem I had was one of the black Turbo CD modules wouldn't play sound, even when used in "Discman" mode with headphones. It came into my possession that way and I never opened it up to determine the problem. For all I know some dumbass kid poured his soda into it. (It wouldn't even spin up when I got it-- this was fixed with some gentle coaxing and a drop of machine oil on the bearings.) I turned around and sold it on eBay to an eBay Store at a profit.
On the other hand, I have heard of many many problems with Duos, particularly the original black ones. Since you're talking Duo-R here I'm not sure how that applies. But just take a look at this forum alone-- there are at least a handful of threads dealing with Duo problems.
In all fairness, I've never actually owned a Duo-R to compare and I've heard the Duo-RX is the holy grail of all Turbo/PCE systems when it comes to reliability.
If it was me, and my choice was the PCE-CD/3.0 system versus a Duo-RX, I'd take the RX hands down. But it's just a Duo-R we're talking here... Is the Duo-R even any different than the black Duos, other than the color?
If it was me, I'd probably ask a question just like you did.
I guess all I can offer you is that I'm one of those who "swears by the original". Since I got my first CD deck 10 years ago I've never had one do me wrong.