droptimo, GameFreak regularly drops features both out of laziness, as well as a way to prevent painting themselves into a corner. If all the cherished and celebrated features become a standard in every game, GameFreak will have to spend a lot of developer time integrating those features into every new region - or worse, designing the region around them. This creates many design limitations, imagine for instance what kind of compromises they would have to take to design Kalos around seasons, so by dropping features they give themselves more freedom. Though, I expect trainer customization to be a staple in future games, and it will possibly be expanded upon in later generations. After all, the player character is meant to be a sort of "blank slate" for gamers to project themselves onto, and trainer customization makes this a lot easier.
Another reason why features are dropped, are - to put it cynically - to make the games worse and less replayable. Pokémon games are lots of fun, but they shouldn't be so fun that you feel that all you ever need is this latest game in the series. If gamers are too satisfied with the games they already have, they need more reasons to switch over to the new games once they inevitably come out. Each game has to be better than the last one, either by content or features. New content (that is, mainly, new Pokémon and an entire new region) will usually trump new features, so the first game in a new generation can be pretty void of features that makes the game replayable (see XY, for instance) - gamers will buy them anyway. However, GameFreak can't just make a new generation each year either, so they make games with old content, but new features to make the game more attractive.
However, by including all the features in the first game in a generation, it is a lot harder to make the next game better. If XY had had a Frontier, Gym Leader rematches, a compelling sidequest such as Contests, Secret Bases, a seemingly endless postgame, and maybe even the DexNav, what could GameFreak use to sell ORAS? Would most casual Pokémon fans even consider buying XY2 if XY had all the features they needed? No, to maximize sales for XY2, GameFreak needs it to be a much better game than XY, and the easiest way to do that is stripping features off XY (compared to, say, BW2), only to re-introduce them in XY2. XY doesn't need those features, it has a new region, a new story and new Pokémon, it would sell like hotcakes anyway. By removing the features, XY starts to feel stale and thoroughly out-played by the time ORAS or XY2 comes out. Suddenly, those new games seem fresh and exciting compared to the boring old game you've played through so much already. You buy the new games, only for them to feel worn-out and dated when the next game pops by. After that, cue new generation with new content, but all of the features mysteriously stripped off again. As a small bonus, you save some developer time for XY too, as you don't have to implement features left and right. This should also explain the lack of a patch for XY to add in the new ORAS-introduced Mega Evolutions. By giving ORAS content XY has not, ORAS becomes a comparatively better game, urging players to buy the newest game if they want all the content the franchise has to offer. Cue a couple of movies or Anime episodes promoting that new content, and kids start nagging their parents about the newest games.
So yeah, it's a mix of keeping their options open, laziness and cynical money-making. In short, don't ever expect a "perfect" Pokémon game. If any, it will be the last game of every generation. Since GameFreak doesn't need the generation-openers to be stuffed with features to sell well, there's no reason to hold content back from a generation-ender. The last games of a generation will thusly be packed with features, intending to keep players playing for as long as it takes to design and develop a new generation - which usually takes longer than the time between games in the same generation. Making the generation-enders replayable is the best way for the designers to keep the games freshly in gamer memory in that news drought between generations.
