Just have a single "Nintendo eShop" for every system. Obviously it would detect which console you are connecting with and only offer you those games. i just find it annoying that dsiware games (even the new ones) can't run off the sd card and the 3ds storage blows

Cool story, bro. If you can manage to make Nintendo make that happen, you'll have the eternal praise of a lot of people worldwide, but until then, sorry you don't like how Nintendo manages its online stores.

As far as I understand, the DSi/DS games & the DSiware isnt run in 3DS mode but instead it is run in a DSmode so unless Nintendo update the firmware on the DSi to run the software from the SD card I cant imagine it being possible to do the same with the 3DS working in DS mode.
Its like having a dual boot PC running with windows and android and being able to expect to run Microsoft Office while in Andriod mode.

This should happen. I mean, Nintendo or the third party developers could publish HD DSiWare to play on the Wii U. Maybe with 3DSWare too, just minus the 3D. I agree, the eShop should be on the Wii U. Also, WiiWare could be played on the 3DS with the new motion controls! Hopefully Nintendo puts the eShop on the Wii U, because the Wii Shop Channel is crap compared to PSN or XBLA.