I haven't seen Captain EO in its entirety since the last time it played in Epcot, but on the basis of YouTube excerpts I don't think it's aged well at all. It seems too derivative of Star Wars, too kitschy and quite possibly marks the beginning of loud, flashy, mindless thrill rides that are gradually diminishing the parks' subtlety and charm (i.e. Body Wars, Mission: SPACE, Stitch's Great Escape, etc). Still, I'd be interested in seeing EO again, if only for sentimental reasons. Otherwise I think HISTA is probably the better show, but as Thrill Seeker pointed out it too is pretty gimmicky.
Magic Journeys, on the other hand, gets my vote for best Disney 3D show period. Sure it has its share of limitations -- the primitive CGI, some flat and stilted visuals, an unshakeable 1970's vibe (which I don't really object to, as it adds an interesting bittersweet dynamic to the film, though some people find it offputting) -- but I feel it's one of the few attractions that truly captures the wonder, imagination, and even confusion of childhood, along with Journey Into Imagination and Mr. Toad's Wild Ride (which incidentally also use a similar dream-like associational structure). Plus its premise is more timeless and captivating than EO, or any of other show for that matter, because it moves beyond the confines of formulaic plots and plugs for popular culture novelties, and instead explores more universal and mysterious territory: the nuances of the human mind.