I really only remember the designs not being liked, and that it was Gen 5 pokemon only until postgame. Which caused people to lash out against specific Gen 5 designs like Garbodor and Vanilluxe (They should be thankful they could still transfer their old ones in to be honest considering where we are now with Sw/Sh)
Those same people would complain about their being a rubbish bag and an ice cream pokemon, and then go on to praise Magnemite and Geodude. Pot meet's Kettle I suppose.
I suppose Pokemon Cycle is partially to due with it is as well. Those that grew up with Gen 5 are in the primary online demographic so they talk about it more.
I do wonder if it happens to Gen 6, some are saying they are seeing it as well now, I don't really see it still. There's like 3 factors to like about X/Y that are specifically X/Y, It's Online (Which is somehow probably the best iteration in the series, what the heck), The Megas (Which are controversial, but people like them and are more vocal about it now that they got removed), and the anime season (Can't blame them, it's a lot better than Best Wishes). I haven't seen anyone go out of there way to praise the characters or the story of X/Y, and ORAS reminds controversial, soundtracks as well feel a lot weaker that gen as well. I dunno what else people like for X and Y specifically. Variety of pokemon as well? I see that mentioned time to time. Trainer Customisation and Amie are popular as well and have remained staples.
X and Y also have the move to 3D Burden which has always been seen as a turning point (Some do see all the changes to 3D as good, but others see it as when the games started to struggle as well), it's also the gen that started going hard on Gen One Pandering which hasn't really left the series since which has made it controversial too. So I dunno about X and Y becoming beloved. It may happen, but I would also say it's going to see a lot more hate than other gens as well.
Wanna know how I know that? Well, people say the Zelda Cycle is a thing, but I'm looking at that Skyward Sword HD thread and there is a hecka load of people in there that hate that game. Zelda Cycle did not apply to Skyward Sword, that's for sure.