As an automotive journalist (and automotive enthusiast), I feel your pain - if the IS250 can be equipped with a manual, why can't an IS F? Too many of the press vehicles we receive are automatic. Nothing makes me happier than when a high-performance car with a true manual transmission is delivered to me. Especially after I get the "manual transmission itch" that comes after driving 50+ consecutive automatics.
That being said, living with a high-performance car with a manual has its drawbacks - heavy clutch in stop-and-go city traffic, relatively frequent and expensive clutch replacement, the embarrassment that comes with missing a shift on a drag strip, etc.
I would choose an automatic if the car was intended to be used as my daily driver.
For a weekend car, no question - I would go with the manual, simply for the reason that I feel more connected to the car while driving. A good car with a good manual transmission provides a 100x better driving experience, regardless of the fact that the certain automatics can outperform their manual counterparts.