Yeah I don't get how people can't see that this is an entirely new console.
The upgrade in graphical quality is minor compared to the GBA -> DS. The DS featured a touch screen and an entirely new layout of screens and buttons compared the the GBA. The DS used entirely different cartridges than the GBA. The DS has a completely different name than the GBA.
The DS and 3DS are so similar that it's really easy to assume that the upgrade is a minor one, especially since Nintendo has a history of extremely minor upgrades. This is especially a problem for casual gamers who might not follow console trends very closely.
Nintendo would have been smart to change the naming convention for the 3DS to not invoke the DS at all. But at this point, they're invested so it's all water under the bridge.
The Wii-U will pose exactly the same problem. People are going to be asking for months if Wii-U games are compatible with ordinary Wiis.