Strangely enough, I think Master of Orion 3 is closer in spirit to the original (and IMHO the best) Master of Orion in spirit.
Master of Orion 2 is perhaps a little too Civ-influenced; I definately enjoyed it a lot more than any Civilisation game, but it felt like it had lost some of it's individuality.
Master of Orion 3 was, at least, unique. It wasn't anywhere near as playable as MOO1 or MOO2, but as a fan of the original Master of Orion, I wouldn't have been much happier if it just built on the more Civ-like MOO2.