Well I'll wade in...
I had a IS200 Sport with 6spd man, it was a beautiful car to drive, gearbox was smooth and like a rifle action, I didn't ever think of driving an auto for 8 years.
Eventually the I could afford a sec gen SE-L. I had tested the new manual diesel, as a courtesy car, found the power a bit strange, nothing, nothing, then all at once and the gearbox wasn't as smooth as the IS200's. I haven't tested the sec gen petrol manual but by most accounts the auto is better, beautifully sooth, and cheaper to tax.
For normal day to day driving, a few miles to work and back, the Auto is King, if you are regularly travelling a long distance then the diesel might suit you, for fuel consumption, it need longs runs, and doesn't do well if you drive it short distances alot.
If you are not bothered by fuel consumption, stick with an auto and choose which model and how many toys you want, good luck hunting.
J.