I own both currently. To me, my 2004 AP2 seems boring compared to the 2001 AP1. I think AP1 has a tire size difference too. Might make a difference.

 

I have an AP1 myself. You're really not going to go wrong with any year.

The AP1s have the 9K redline and a significantly different suspension feel as they're firmer. They are more prone to spinning out as they're more neutral.

The AP2 has a 150cc bump (US), and a shorter primary reduction gear. The torque difference from the engine isn't significant, but the shorter primary reduction helps a bit, too. 150cc isn't going to give you 'night and day' difference. The suspension is softer and more forgiving and will understeer a little more, and if you're new to RWD that may be a safer way to go. Outside the US, the AP2s have the 2.0L, but with the shorter primary reduction, so you get most of the torque/mechanical advantage, and still get the 2.0L engine.

The 06-08 adds a tuneable ECU. This is a big plus, but these cars sell for a premium. They're also the softest and safest S2Ks, and have stability control. It's really up to you as to which you want, as there IS a difference depending on what you're looking for. The returnless system is only going to limit you if you want big power, like 500.

My own is an AP1 with a CR suspension and a SOS supercharger that I've had over 10 years. It is very firm, very responsive...and also way more likely to spin out if I do something stupid. I wouldn't have it any other way.