Hmm, then it's a tough choice. My main bias against kensai/thief was gonna be "no armor", but that's turned out to be irrelevant.
Still, I'd say fighter/thief (I assume you mean multiclass with this and not dual-class). You've already given the reason yourself: they get the high level abilities for fighters as well as those for thieves. Kai isn't that great, IMO, and the bonus to THAC0 of a kensai will probably be offset in the long run by the extra fighter-levels that a fighter/thief will get. The -2 AC and weapon proficiency beyond specialization (**) is the only thing that speaks for a kensai, but that doesn't weigh up to the things I just mentioned, IMO.
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