There is some of that yeah, but it's not as contradictory as you think. As far as "third versions", the fans mean they want a followup to the original game with expanded content. But that's a mouthful to say over "third versions", so they just say third versions. But really, they want something more like a sequel that offers much larger expansions than traditional third versions, which neither XY nor SM got. Hence people are complaining about both for different reasons. Doing new things to shake up the series is good, but mechanics like Megas and Z-Moves are kind of tacked on and overcomplicate things so they're not really "shake ups", they're more like regional flavor which is not what fans want, they want progress and changes in philosophy, something Game Freak has been very resistant to lately (and arguably has never really done).
Game Freak's problem is a matter of balance and execution, they've been pretty good at changing the things the fanbase wants changed, but not in the way they want it changed. So their solutions just fragment the fanbase even further. They don't really "improve" things, they just come up with some contrived solution for the sake of "uniqueness". For instance, in 4th gen people complained about the amount of cross gen evolutions in the dex and how the old Pokemon have too much of a presence, so what do they do to solve that in 5th gen? They removed cross gen evolutions altogether and limit you to new Pokemon only in BW. Which of course people complained about, so then in XY they had a ton of old Pokemon and they pair that with Mega Evolutions as a solution to the lack of cross gen Pokemon. But the fanbase didn't like that either because now the old Pokemon are too much again and Megas are only a temporary power boost which doesn't help some of the weaker Pokemon. Do you see what's going on? They're overcorrecting the problems and flip flopping between opposite extremes, which triggers one side of the fanbase or the other (or even both). That's not a result of the fanbase having different preferences, that's a result of Game Freak failing to fully address the issues.