The S2000 had a long production run, but is now out of production. Though a decent car it is not rare. The latest examples had better steering so are better to drive.

The GT86 and BRZ are new models, basically the same car with different badging. There are a few trim options, such as leather and sat nav, which you need to have. Whether to go for the manual or automatic is a personal decision. In the USA, probably better to go automatic because that increases the number of potential buyers. In the UK probably better to go manual.

Something you might not expect is the lack of torque in the higher gears, requiring downchanging if the speed of traffic drops on an incline. I can't tell you how well the GT86 and BRZ will hold their value. I can tell you that in the UK there are fewer BRZs.