I'll add to both Bob's and Rick's comments. The green top tends to require a little more work (and in some cases a whole lot of work) getting the interior surfaces smooth. It's not a really big deal if you have an orbital sander and apply a little filler. Aerosport Products also has a headliner that you can use that will hide these imperfections and reduce the amount of work you'll need to do on the top. There is no right answer here, it just depends on your personal preference and the way you want to finish your interior.
Like Bob mentioned, there are differences in the pink top too that only come into play if you are installing an overhead console. Making mods to accommodate the green top or the other pink top isn't a big deal either. It may take you an extra hour of work to make the modifications.
I do agree with the previous comments that it isn't a factor in the deal. One might argue that an older kit, that just happens to have a green top, you may be able to negotiate a better deal. Not due to the top, but more to the age of the kit and why the builder has chosen to put it up for sale.
Bob