Ummmmm that Tsukuba straight doesn't look long? Take a look here
http://www.jasc.or.jp/outline/index.html . It is a 433 metres long straight and is one part of the circuit where faster straight line cars always have a chance to overtake the slower ones.
I also don't agree that the AP1 has such a big difference with the AP2 although obviously AP2 is slightly less nervous. My point was, even when the Japs were driving the AP1 they already unanimously gave it the vote as a top driver's machine with great at-the-limit control ability whereas the local journos bagged it for being too nervous and twitchy. The way I look at it is however, even if the S2000 is twitchy at the limit it actually won't bite like an MR2. Its twitchiness is its advantage because the top drivers can extract the most out of it!