Seeing how they recently merged their hardware divisions, it would make sense Miiverse would be an interhardware network, since the goal of the merge was to have higher synergy between handhelds and Consoles
i for one prefer to have both miiverse work together.
edit: just to add though. i'm hoping nintendo will release a system update for the 3DS that will let us "convert" our accounts from using the friend code to a Nintendo Network ID. i don't care if the ID is attached only to 3DS accounts. or perhaps later, they can allow you to use you Wii U NNID to work for your 3DS also.
Really good article, but I believe they won't split Miiverse in 3DS and Wii U versions, because that second image suggests it'll be one big service for both systems, one of my thoughts is that It'd be confusing to have 3DS games in Wii U's Miiverse and vice versa, but It could be simply solved with a filter. The friend code thing is the only problem, but It can all be adapted with a big system update. Also, there will be a smartphone version for the Miiverse, implying it will be one service for 3DS and Wii U that can be accessed via smartphone, I believe it won't have an option like "3DS Miiverse" or "Wii U Miiverse" to sign in. Many ideas for new features I believe won't be added, but some of them are possible like 3D posts and stuff, I think they should increase the characters limit too. Just my opinion, though.
edit: just to add though. i'm hoping nintendo will release a system update for the 3DS that will let us "convert" our accounts from using the friend code to a Nintendo Network ID. i don't care if the ID is attached only to 3DS accounts. or perhaps later, they can allow you to use you Wii U NNID to work for your 3DS also.