I concur with the above. My old supe was an auto, and I used it as an everyday car. It was a stock TT (not anymore though now Mark Newmans had his way with it ) and it was a beautiful drive. Stress free cruiser with the required perfomance when needed.
I now have a 6sp BPU, the BPU 6sp is a much more hardcore car, and would no doubt do nothing but annoy the pants off me in stop start traffic. However this one is a weekend toy, so it's perfectly fit for purpose. It's a much more involved drive than the auto, but I'd not enjoy it as an everyday car. The 6sp box has quite close ratios, so I find you shift a fair bit more than you would a normal family saloon.
If you use your car everyday and do a fair bit of stop start traffic, stick with the auto.
If the supra is not your main form of transport, and you want a manual for a more involved drive, go for it.