I'd love for customisation to remain, but I think assuming that it not being in the remakes means it's not being carried forward with other new games would be a bit drastic. Given that they're remakes, I wouldn't be surprised if they didn't change as much as to include customisation/amie/things like that. It all depends how heavily they're updating it - if it's just a visually updated 3D port of sorts, or if the whole gameplaying infrastructure is being overhauled and given all the new bells and whistles we had in XY. At the moment I can't say I massively mind either way since my biggest reason for wanting remakes was an update on the visuals for such a beautiful region, so I'm not going to let myself expect anything more than that.
Bottom line for me would be that if I see that they're including other new features we've had, I would be very disappointed and surprised if customisation wasn't there too. Otherwise, I wouldn't be too upset or shocked if we were left without it - there's still plenty that we've actually not been able to have in newer games, like contests and bases, and if they at least keep those it's still something different from what other recent games have offered.