40-50mm will have no difference in clarity on the same model(ie:VXII 40mm or VXII 50mm). It will give you 2% more light gathering capabilities! Is this important and worth extra, only you can decide. My best advice is try a 40mm and 50mm at fading light times to see if it will matter to your hunting situation and eyes. Also keep in mind the mount height it will require to for a 50mm and if that will cause shooting form problems. If so then 40mm is the way to go. Some guys swear by either, so I believe it is more personal than functional for the mpst part.

As to which scope I would choose if funds allow the new VXIII in whatever size objective you want. It will be both clearer & brighter than the VXII, offers many enhancements and comes from the rock solid Vari X III line, which was lagging in technology the past few years but has always been regarded as a good solid scope. If your talking Vari XII or Varix III, then the III(in case your finding it used or on ebay, etc) would be my choice hands down. Also it is always better to buy better glass(ie VXIII 40mm) in a smaller objective than bigger objective in lower quality of glass(ie: VXII 50mm), again when determining budget and options.