Hmmmm... both have their advantages and disadvantages.
Kensai->Thieves have Kai, an AC bonus and are able to grandmaster in their weapon of choice.
Fighter/Thieves can share from both the Fighter and Thief's high level ability pool.
I am partial to the Kensai->Thieves though.
Kai + Backstab + STR + ToB Quarterstaff =
Woah...