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It's the same here. Interesting that, since Emerald's been out for so long now. Emerald doesn't exactly come with anything extra in its box, so that doesn't technically make any logically sense for it to have a higher price.
Maybe they're trying to move us all to 4th gen by setting the price lower than 3rd gen?
Game, a Video Game store in the UK, usually sells most of it's Games at Recommended Retail Price, and they're selling Diamond and Pearl for £30 ($43.80), and Emerald for £20 ($29.20). either they're different to the rest, or the RRP price for both those games is different in the UK.
I got Emerald new at target for $25.99 and I saw Diamond and Pearl were both $42.99 so I dunno if some other places have Emerald priced higher than Diamond/Pearl.
It really depends on the area. Where I live, D/P costs $34.99 and Emerald is $24.99. I have seen one go for $39.99 though. Semi-related, why do most DS games stay at like $30 even after almost a year? Specifically, I'm talking about Kirby: Squeak Squad.
They are still in production. The only discontinued Pokemon games are:
Red/Blue/Green/Yellow
Stadium
Gold/Silver/Crystal
Stadium 2
Snap
and I believe Super Smash Bros. 64. Not really a Pokemon game but it has Pokemon in ti so, yeah. This also explains why its so hard to find a copy of R/B in stores. *sigh*
Then, the answer to why R/S/E are still priced the way they are is probably as simple as "because Nintendo knows they can". Handheld Nintendo products are still hot and in demand. So from Nintendo's point of view, there's no point in depreciating the value of things that are still popular.
Plus, the need for certain Pokemon that can only be caught in the GBA games could be a reason. I mean, for those who actually try to have a living PokeDex instead of cheating/hacking. Although, Nintendo would have to be evil masterminds to think of that.