Gen IV and V are no more similar than IV or V.
I didn't state any proof, just showed some evidence that makes the incompatibility claim suspect. To add to my original points that 3DS can send a DS Download Play and communicate wirelessly (and via IR!) with a DS, it also doesn't make sense based on Nintendo's history when DS was the new thing. The DS games (D/P/P) had no problem using the GBA APIs -- it even altered the GBA save files!
Also, you need to understand that the core libraries for the DS and 3DS are stored on the console, not the cart. Though if they were stored on the cart, there's nothing preventing them from being added to X/Y's cart. Since libraries are just compiled code and no assets, they're small.
The only possible way that it could be truly incompatible is with short-sighted design of the 3DS. It may be impossible to load both the 3DS and DS APIs simultaneously. Putting the DS APIs on the cart would also be not impossible, but a very bad idea (a hack) which could cause problems down the line with future revisions of the 3DS.
That explanation seems kind of flimsy to me. You can see why I think it's "won't", not "can't".
But to call it a conspiracy theory is to take it too seriously.
Unfortunately, Nintendo has earned itself a reputation for unnecessary nickel and diming in the past, so heh...