I don't find them too similar (at least in the vintage version, I have not smelled the reformulated HB, but just the flanker Nuit Bleue or something like that, which is different). Of course it depends on the comparison group. Relative to most modern feminines, which are either shrill white florals or pink syrups, they do have the mark of another era: complex, but smooth, almost velvety, rich, natural smelling, they envelop the wearer rather than assaulting the nose.
But to me Mitsouko is a smooth chypre, bitter, mossy, with the fuzzy feel of peach skin, while Heure Bleue is a serene heliotropin-orange-spice floral. One is elegant in a sort of French, uptight way, the other is smiling and a little nostalgic.
The usual comparisons are with the Cotys which likely inspired the Guerlains, that is, Coty L'origan versus l'Heure Bleue (and in part Apres l'Ondee), and Coty Chypre and Mitsouko.