Separates usually allow the designer, given a relatively large budget to work with and some free reign of topology/technology choices (latest tech isn't always the best in absolute terms when it comes to digital), options that all in one solutions can't possibly accomplish in all but the most costly of universal players (even then space limitations do force compromise separates don't have to deal with). Sometimes these advantages yield better results and sometimes they don't, it depends on any number of key factors, price being only one of several considerations.
That dependency hinges upon which manufacturer you choose. Esoteric, Linn, Classe , Ayre and few others all make very very good Universal players but some of those same manufacturers have separate unit line ups that eclipse their one box solutions by a fairly good margin. The cost can be prohibitive to all but the deepest pocket of audiophile regardless of which solution you opt for. Lower end separates do tend to be a better value for money but the choices you have to make in order to best a competently designed single box solution must be made even more carefully in these price brackets. There are gems to had at every level, the hard part is knowing what they are. SONY's latest ES series SACD/CDS player is one of those rare instances where a large company get's it right (IMO). That doesn't happen all that often, what's even more curious is the fact that SONY dropped official support for SACD a couple of years back....I guess loyal SONY customers must have berated the companies management long enough for the SONY engineers to reward their customers with a top shelf affordable SACD/CDP....is it better than a 3.5K separates setup ?...maybe..maybe not. I've never been enamored by SONY's house sound anyway so for me it's a moot point. Hopefully SACD is making a quiert comeback ???? Could be the result of the Blu-ray medium taking hold and stressing an equal emphasis on picture and sound quality. IMO anyway.
Peete.