i have owned my MY2004 Spider for 4 months now and extensively test drove both TS and JTS engines.
The JTS engine i found to be a vast improvement in terms of low end torque and pulls more strongly when cruising and taking off at the lights. The induction sound i think is excellent and mroe refinded than the TS. Power is up on the TS and it is noticeable IMHO.
I highly recommend getting the update Spider with the JTS engine, i think they look better and the glitches form the previous model have been rectified.
The JTS loves a good fully synthetic oil changed at no more than 10,000km, the recommended by Alfa of 20,000km is far to long and Alfa have revised this.
Full service history is essential in these cars.
It comes down to what you like really, if you like both definitely go for the latest Spider you can afford.
Hope this helps Cheers Josh
PS As for the V6, i personally could not justify the price premium nor parts expense, you can have much fun in the 2.0ltr!