They could set it up so it displays both screens on the gamepad. That might not be half bad.
They would have to do it side by side, but that would still be too awkward. Quite a few games require measuring up the bottom screen with the top screen for accuracy.
Also, we still don't know what they'll price these games at. It might end up being cheaper to just go to the store to buy a copy. Or used copy even. Just about everyone already has a 3DS which is backwards compatible, or if not, then a regular DS/lite/i.
The only games I can see working out with the Wii U gamepad are puzzle games, like Brain Age. Do that's likely their main focus if anything. I don't think anything else would even work half as decently as it would on an actual DS, without them having to restructure the whole game and how things work.