I've owned the R-D1, and while I like the idea of it, I just don't find it good enough when it comes to image quality. I know such a statement always releases the flood gates of opinions what is good enough and what isn't. All I can say is that I owned it in 2012 after I had been owning other more modern cameras, and going to the R-D1 just doesn't cut it for me personally then. I had simply gotten used to better quality, wether I needed it or not.
In use though it's a very cool camera, if there was a brand new one released I might consider it to be honest, but it needs a modernized sensor.
In any case, I finally ended up with an M9 that I purchased used. My opinion on the M9 is that it is a lovely camera, if you can afford it and if you really want a rangefinder. However, my opinion is also that no matter how you twist and turn it, it is severely overpriced. Yes, it is great build quality, but I still don't consider a $7000 price point appropriate. Again, perhaps also an opinion that many people don't like.
Anyway, I purchased it anyway because I did have the money and I really wanted it - I love that camera. Do I think it is worth the money? No. Do I think the alternatives offer good enough quality? No. So - I don't really have a choice, for me the M9 is still the best option no matter the price. I might get the M one day when the prices have dropped on the used market, maybe I won't.
In any case, when it comes to your original question, I don't think it is a comparison that can be made realistically. There is only one single common thing between the cameras in my opinion, and it is that they are both rangefinders.
If you are happy with the 6mp sensor in the R-D1 and all that it means, then that is the better camera. If you aren't, then the M9 is the next cheapest option in my opinion (someone would probably say the M8 is the next option, perhaps it is, it wasn't for me for other reasons).
Other than that, to be honest, I find it a pointless comparison. The two cameras just differ more than they have in common in reality. I could go into details on what I like and dislike with both of them, but it still doesn't change the fact that I think they aren't really comparable..