It think they definitely will. However Im not quite sure on what level they will be desired. Whether it will be just collectible to Toyota die hards or if it will be desired by people who love iconic Japanese sports cars. Nonetheless there is no doubt the MR2 of any generation are special and a true automotive enthusiast recognise this whether they like Toyota or not.
With that said...I think it will only be the "special editions" (those that were slightly changed over the original) of the MR2 that will be truly desired. For example, the revision 3+ hardtops will certainly be at the top of the list along with the Bathurst model and the GT models etc. not far under.
But who really knows....we'll just have to wait and see. But even if they arent that desirable in the future; I will certainly be holding on to mine as I recognise how special they are and love all their quirks which include how challenging they generally are.