Sure, skin deep, it's the same. But, when you look deeper, it isn't. Just like the monsters within, Pokémon is a game of progressive evolution. Comparing Gen1 to Gen4, here's what was added over the years:
-Dark and Steel types
-Split of Special stat into Special Attack and Special Defense
-Genders for more than just the Nidoran lines.
-Baby Pokémon, breeding, egg moves
-Held Items
-Natures
-Abilities
-Double Battles
-Diving (granted, this was ignored in Gen4)
-Contests, Pokéathlon, and other such side-activities
-Online
-Complete change in the Physical/Special split
Even excluding the additions of attacks and monsters (including a greater mix of dual-types), a lot has changed over the years.
Gen5 will likely continue this trend. There will be more changes and balances in the battle system (say goodbye to the Gen4 metagame and archtypes) and more side stuff.
And the stories? They're fine as they are, just a small motivator as a means to an end. Pokémon doesn't need some grimdark, "EPUK" storyline about some great evil, world destruction, and salvation and such. Let Pokémon be Pokémon, and Final Fantasy be Final Fantasy.
How much of that CHANGES anything? Video games in general have evolved to be more complex as well. Graphics have improved, systems have become more powerful, controllers have mor buttons. But releasing Space Invaders on the PS3 and adding a few new controls, graphics, and formulaic functions doesn't change "shoot up, kill aliens" does it? This is the problem that many developers face, actually, as people are less tolerant of the same formula copy and pasted to new games. New generations require new innovations. Adding lots of accessories to a car doesn't change the performance of the car if you don't do something about the engine, it just weighs it down.
And, Pokemon has slowly been becoming darker as well. Think about the last few generations storylines. It went from Team Rocket trying to cause comic mischief to Team Galaxy literally trying to destroy the world. And let's not forget Team Magma and Team Aqua trying to literally sink the continents or raise the oceans. There are Pokemon gods, side dimensions, evil villians attempting genocide! And yet, because the formula hasn't changed to support these new additions, they became superfluous. In the end, it is still just "beat grunts, explore dungeon, get item, beat boss" and "start in small village, catch Pokemon, beat rival, level up, beat gym leaders, beat Elite Four". Who cares if you have to hold an item to do it now instead of using an item? Does it change what is on the other side of the equal sign? No.
If I participate in a beauty contest, I get a ribbon in my Pokemon's status viewer. But these things are mini-games that usually have no bearing on the main game other than to add some time to the game if I choose to participate.
I don't want Pokemon to be Final Fantasy. I want Pokemon to be Pokemon, but a new version of Pokemon. Not the same version with prettier graphics, slightly different (yet essentially similar) Pokemon, and the same linear progression through the storyline. They don't need to change any of the additions they added, or even the storylines themselves, its just the presentation and propulsion that need changed.
However, what it really comes down to is who will or won't buy the new games. If you like the repetative sureshot nature of the Pokemon formula, then by all means, please buy the game. But that doesn't mean I have to agree, or have to buy the game. This is the ultimate measure of a game's success. Not my opinion, which may or may not be shared by anyone but myself.