Responding to the original question, I have a BDP-2 (with the new output board) and BDA-3 . I like the idea of the streamer and DAC being separate. I feel the shelf-life of a DAC is longer, and I would be willing to pay for that.
However, a single-box has the advantage of better connection between source and DAC (no need for USB, AES/EBU or S/PDIF). This could result in better sound if the rest of the components were comparable.
I love the sound of my system with the AES/EBU connection. I do not like it with USB. I upgraded my speakers recently, and the difference is even more noticeable. The USB is a flatter soundstage. The harmonics are fine, but the sense of space is greatly diminished.
I also notice a difference between Balanced and unbalanced outputs (though of course, that takes into account the preamp inputs and different cable brands as well). That one isn't a better/worse thing, more of a preference. The Balanced sounds a bit disembodied but more full, while the unbalanced has a more focused soundstage, but perhaps slightly less full. Honestly, I've read that this is a common difference on other systems, so perhaps I can't make too much of it.
So for me, I want my separates, but I also want the best sound. I can't help wonder that if Bryston supported the use of an external master clock for the BDP and BDA, we might get even better sound.