Gamestop trade-in prices aren't just affected by age of the game, but also how much they have/need in stock and how quickly the game will move. This is why something like FF13 is worth nothing (because no one wants it and they plenty of stock) while Dark Souls is worth more than titles of similar age (It's in demand so they always need more). Pokemon games have similar issues: People still want copies of Diamond and Pearl to transfer their Fire Red and Leaf Green teams to the DS series, but D/P took a bit of a hit when OR/AS hit because you didn't need to transfer R/S pokemon through them anymore. People still want those titles to get legitimate versions of Jirachi (along with the gamecube disc that lets you spawn them) but that's about it.
So yes... older Pokemon games are less valuable at Gamestop, but some are always going to be in demand for particular uses.