We do a fair amount of Blu-ray Disc duplication and seldom hear about problems with compatibility. I think the biggest concerns are about the difference in the format of BD-R and BD-Rom/replicated Blu-ray Disc.
Keep in mind that right now, Blu-ray Disc is quite a bit different than DVD, in that the duplicated format is very different than the replicated format. Not only is the process of getting the content onto the disc different, but the features and options available when authoring them are different.
Currently, you cannot copy-protect a BD-R. With what I think are very few exceptions, you cannot use BD-Java on BD-R discs. There are some other limitations too, but those are typically the biggest things that I see as restraints when comparing the two.
If you are careful to encode your video assets well and in spec, and author the Blu-ray well, and in spec and do some testing up front with your master, a duplicated BD-R should have high compatibility across the majority of players on the market.
Even some replicated Blu-ray Discs still have problems. I am going back and forth with Netflix right now trying to trouble shoot why the Mad Men Season 1 Blu-ray Discs don't load on my LG-BD390. They have sent multiple discs, and they all have the same problem. Sometimes it just happens.