The CD3 is out of production as far as I know.
I beleive this statement is incorrect.
In any case, I have not heard X-03, but I do own CD3 MkII.
I like it a lot. I think it has a very good transport. The only problem for some people may be the fact that this is a top loading player. Aside from this, performance is really really good. Especially when run through its XLR outputs into a balanced preamp. To me, the CD3 MkII is a much better player than DV-50S, although I haven't heard this one in my system, I heard it plenty of times to come to conclusion about its sonic character. Very good player, but in my opinion not as good as CD3 MkII. If you have a lot of SACDs to play, then may be you should consider Esoteric. Otherwise, ARC player would be my recommendation for redbook playback.
Also, check out the review of ARC where it gets compared to separates as well as Esoteric X-01.
this is ARC review http://www.soundstage.com/revequip/audioresearch_cd3mkii.htm
and this one is a review of X-01