I've put my Pokemon in Isle Avue and just got Isle Evelup, but have seen nothing change about my Pokemon in Avue and don't quite understand what Evelup does, so what do they do, and is there any difference when you develop the Isles other than more Pokemon at the Isles?
Isle Evelup is for training base stats, this is like EV training. Up to six Pokemon can participate. You can give them a drink which will boost the corresponding stat. This does not level them up. Also you can set a timer in which how the the Pokemon will play. Adding pokebeans speeds up the time it takes to do this
Isle Avue serves for two purposes. First it is used to increase friendship with your Pokemon. You'll be told different statements to show how much friendlier your Pokemon are. Also it can be used to hatch eggs. Adding pokebeans can increase the rate at which eggs hatch and make you Pokemon grow more friendly faster.
Source: experience and http://www.serebii.net/sunmoon/pokepelago.shtml