the black box is the stock box, the two plates with filter in between looks like the R&D (maybe the power plenum)
frankly, unless your running aftermarket items like a pipe/carbs& such, the stock box is the better choice, although the aftermarket filters like the r&d do offer more aesthetic's, they do very little, and at least the way I learned it it was really not necessary, and the R&D IMO is a big fat pain in the azz because its not much easier to remove than the stock box when you need to do some carb adjustments.
IF and when using AM filters, my personal preference was Prok's, they looked better and offered much better access to the carb adjustment's, but in the end I was really just pissing away $100 and making my ski look a little prettier. I hated the R&D, I removed mine, added prok's, blasted & painted the r&d then sold it on ebay for about $40.
one last note: the carb's were likely re-jetted slightly due to the r&d on that ski so keep that in mind if you decide you want to make a change and go back to stock. However, there's no pressing reason to do such a thing, I would just leave it be.