I can't answer your question very well, as I'm a newbie to the Boxster realm. I am in the process of finding the right 00-02 S.
But, I just wanted to say, "Hello," to a fellow CF member. I'm over there, on Off Topic, a lot. I use the same screen name there. I sold my 94 LT1 6spd last May.
I personally would not buy a standard Boxster, but that is just me. There is certainly nothing wrong with them and, if you wife doesn't care too much about performance, would likely love the standard model. That said, you might get more fun from the S.
I can't speak about the color, except to say I don't really like most green cars.
But, hey, we all know what they say about opinions.
I also believe you would find the S to be a little easier to sell, as people to seem to clamber for the used S cars. (Just my own limited experience, though, again.)
--Jaclyn