A change like that seems unlikely for Nintendo, they seem set on using the more user friendly 'block' system. There seems to be some conflicting arguments on the size of individual blocks, from what I gather 8 blocks = 1mb so if that's correct you can work out the size of a game on your own without Nintendo changing their system.
As far as i know they are compatible as both are nintendo eShop, however the amount can only be used on either the 3DS or Wii U eShop at one time, the amount stays with the version of eShop you reedeem it with. You cant switch them between Wii U to 3DS and vice versa.
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