The Xbox and PlayStation systems have a handy little profiling system that links purchases, account info, etc. to one profile, so if you need to replace a system, you can easily access everything you've already bought, your Achievements/Trophies, and the like. It's not so much the same with Nintendo's consoles, which associates purchases and account information with the hardware itself. So if you want to buy a new device, like a 3DS XL to replace your 3DS, you have to manually transfer your information between the devices. It's a pain, and no one has really liked it.
Nintendo is "very much aware" of these complaints and demands to unify the Wii U and 3DS account systems.
"We don't have anything new to announce, unfortunately, other than we've definitely heard that feedback many times from both inside and outside the company," Dan Adelman, Nintendo of America manager of business development, told Destructoid. "It's definitely something that we're very much aware of."
"All development for the infrastructure really happens out of Japan, so we've kind of communicated this need in the market, and they're very much aware of it and working towards really just always improving the eShop," he added.
Of course, this doesn't mean that improving the eShop automatically equates to unifying the accounts. That would be too easy.