Incoming massive wodge of text that probably goes a fair way towards confirming my Nintendo fanboyism.
Interesting you should say that. IMO Pokemon has not changed, and that is exactly why it has lost its way. So, pretty much exactly the opposite opinion. The formula has remained the same forever - get some badges, fight off the bad guys (which apparently can be done just through Pokemon battles, it's not as if they ever turn round and say "So what? Our pets got beaten up by some cocky ten-year-old's pets? How does that foil our plan for world domination exactly?"), beat the E4. You're basically playing the same game over and over again, the only thing different is the Pokemon, and even then several of them are becoming clones of previous-generation Pokemon (though in fairness this is markedly less true of gen VI). It just doesn't seem like Game Freak are ever going to offer us anything different in terms of game design, their efforts go mostly into Pokemon design and battle mechanics.
I will readily admit that deviating from the formula or doing something different might produce a worse game. The example I always give is Pikmin 2, which to me, was not nearly as fun to play as its predecessor. For me, Pikmin 2 felt a lot like playing Diablo, but with Pikmin (hopefully anyone else who has played both these games will understand what I'm talking about), as most of the game was spent crawling through underground dungeons, fighting off monsters with your Pikmin, and there was relatively little of the puzzle solving / exploration / multitasking / resource management elements that made the first game so fun for me. The fact it was largely underground also took away from the bright, even slightly trippy feel of the Pikmin overworld. But still, I welcome that Nintendo developed it. Rather than just remaking the first game with different puzzles they decided to throw wholly new gameplay elements into the mix. What's the point in remaking the first game when I could just play through that again? (Then again, what's the point in making Pikmin 2 when I could just play Diablo?)
On the other hand, take Super Mario Sunshine. This game was more different to Super Mario 64 than anyone expected, and, while I know it's sometimes thought to be a bit of a black sheep, it's honestly bucketloads of fun. In fairness I feel the reason that it isn't as universally lauded as 64 and Galaxy is because it is so different that people don't know what to make of it. Obviously FLUDD has the biggest effect on the game, and most of the levels are designed with it in mind, but the number of ways it can be used stop it being too repetitive; it also allows you to think outside the box and look for less obvious routes through levels, in a way that I never really got again in any game until Portal came along. Voice acting schmoice acting, that seemed out of place, but even the attempt to go beyond "Peach has been kidnapped? Oh noes!" is pretty laudable. After Super Mario 64 basically invented the 3D platformer it might have been tempting to make a clone. And if they had, we would never have got to fling Mario around with his water-filled jetpack and the world would be a poorer place.
If Game Freak did this? Well they might produce another Pikmin 2, a game that totally misses the point of the franchise it represents (yeah, maybe I should stop bashing this particular game, it's not that bad). Or they might create something really cool and innovative. If the former happens? Well, it's still different, it might appeal to somebody. If it's a success? Great, I would hope that would give them the confidence to play things a little less safe in the future.
However, I won't hold my breath. Pokemon X and Y are getting good reviews and healthy sales. Maybe if Pokemon were not a third-party series then Nintendo would take a few more risks, as they would still have other franchises to fall back on should they turn out an unsuccessful experiment. But, since nobody would have even heard of Game Freak if it weren't for Pokemon, they really need every game to sell. And so far it seems they will achieve that most reliably if they don't change a winning formula. So Pokemon games will forever remain the same. Which is a shame.