The AP2 isn't as fun as the AP1, nor does it sound as good. But it's also more tractable and they do tend to put up better track times. They're surprisingly quick if driven well and amusingly slow if not. It's the best gear shift of anything non gated. You're probably on the upper end of "low miles" for keeping it and seeing it appreciate greatly, but if you kept the miles down, you'd always get your money out of it. I'd probably just get an ND over one to not have give up modern amenities and safety bits, plus the passenger side of the S2k is more cramped, and even though my wife is short and doesn't drive a manual, I don't want to find a reason to have to sit in that little hell hole.
I have many stories of making a Miata work as a daily for a few years. Includes holding onto framed art over my head while driving a few miles from the framing shop. Loading groceries into the trunk, around the parcel shelf and over my seated ex. Driving to the inaugural Indy F1 race with a large friend with all of our camping gear too. Learning that the vMax of the roof cover was about 118mph and just how far you have to circle back to find it once it departs. I miss that dumb car more than most, and I'd certainly miss it more if it had been an S2k.