That's like saying that playing every single version of Mario is the same because it's all the same game. And it's not. The newest games do indeed trump the others in most aspects. Just compare Gen V to Gen IV which were both on the same exact console. Gen V is better in terms technical aspects: It runs faster and with more going on. In both battle and in the overworld. And they're both running on the same exact hardware. Additionally, Gen V is truly the first time you're playing the "same exact game" since you start out with a completely new set of Pokemon and are stuck with it until the end of the the main quest. All the games before Gen V could be compared to expansion packs where you get some of the same old Pokes you always had but with the addition of some new ones. Black and White were truly the first "new" games in the main series since the beginning.
Also, the old games were glitched like crazy.