I would lean towards a coax that does not have a separate internal horn or waveguide. For one thing, while not perfect the edge of the woofer cone and adjoining frame/baffle is probably a better "mouth" than is the sharp edge of an unbaffled horn or waveguide. Next, using the woofer cone should give good pattern control down to the crossover frequency, which I think matters. Finally, the horn or waveguide itself is a diffractive obstruction in the path of the woofer's output, and may well be a source of coloration in the upper end of the woofer's range.
I'm a bit leery about the long "snout" that, in most cases, the compression driver's output must pass through to reach the woofer cone. Big Tannoys and several B&C drivers use the same magnet for both woofer and compression driver, which significantly reduces the snoutlength - but that format may be more prone to flux modulation. Which is the more audibly significant issue, I do not know.
As for whether a separate horn or waveguide is better than a coaxial, that depends on the specifics and on what the top priorities are for a given application. One of these days I hope to spend some time working with a good coaxial, as there is a certain undeniable elegance to that format.
Duke