Originally Posted by
j_factor
I think there's a lot of little contributing factors.
There's no new Shining Force. Shining Force 1 and 2 and CD were worth a bit more back in 2004-05, when Shining Force was ported to GBA and Shining Force Neo came out for PS2 (although it's not a "real" Shining Force game). You see old games go up and down in value like this all the time. Nintendo and Square Enix are hot shit right now, so their old games aren't going down.
All the compilations, like you said. Who wants to pay $40 for an old RPG when it's available on a disc I can pick up at Gamestop for like ten bucks?
I don't have numbers to back it up, but I'm pretty sure Shining Force, Phantasy Star IV, and LandStalker sold significantly better than the likes of EarthBound. In fact I'd go so far as to say Sega's RPGs in general were more popular at the time, save Final Fantasy. The Genesis RPGs were (relatively) well-promoted games, with pretty accessible gameplay and style. They weren't arcane or "too Japanese", or released by a little-known publisher.
The types of games that we're talking about, on SNES, tend to be later releases, as compared to Genesis. Nothing like Harvest Moon was coming out for Genesis in 1997. Instead, Genesis got The Lost World. Which is a good game, but it's an action game, and a movie license, and published by Sega. Harvest Moon was an unknown name, with an unknown type of gameplay, by a fairly unknown publisher at the time. The Lost World is still worth a bit more than the average Genesis game, owing to its late release. But Harvest Moon is worth tons more.
Finally, Genesis games are much more easily found complete. SNES boxes felt very throwaway, and so were often thrown away. I know the OP doesn't talk about completeness, but I think this has an overall distorting effect on pricing.