I think it's already pretty clear that there will be RSE remakes. Just look at the similarities:
Sinnoh brought back the day/night feature from GSC, and low and behold, a remake was made.
Isshu is revamping weather status and from what we know so far, probably making it of more significance in-battle and in the overworld as well. RSE introduced weather. So it is very likely that there will be remakes already from the info we know so far.
But let's not get too ahead of ourselves: BW isn't even released in Japan yet!
Getting back to Wally, if he did appear in Isshu, I am sure he could be found at that "shrine", what with his whole theme of closeness to pokemon, serenity, finding oneself, and the like. It is questionable whether you could battle him, but it depends on how GF remakes his character in BW. If he has grown increasingly outgoing as it was shown in RSE, he might be determined enough to battle you. But, of course, that is highly unlikely, since the question arises for newcomers: "Who is this guy, why is he challenging me, and why are his pokemon so strong?!"
So GF would either have to make him un-battleable or lower his pokemon's level significantly, which would then sort of ruin it for the veterans who know who he is.