Most likely yes
Now that Nintendo is FINALLY embracing online connectivity in games, you can bet that there will be a better focus on improving their online infrastructure for games and store.
This costs money to both do and maintain, so for better online connectivity, you can bet they will charge (especially when sony and microsoft do it).
However, I do think they will also include a FREE version. One that will be distinctly worse than the paid version. This will keep them at an "advantage" compared to the competition, but will also look more appealing to kids (no source of income) which is their target audience. The hardcore gaming community will still appreciate the option for better online connectivity and the casual crowd will appreciate the ability to choose cheaper options