Considering Miiverse had a bit more going than just a "glorified webapp" (such as doodle comments and screencapping), it would make sense that the Miiverse would integrate with the 3DS at an OS level. They would have to make it so you can screencap your games and post them on the Miiverse with relative ease. (Most likely the Miiverse would appear along the row of icons where Game Notes and Friends List are.)
Don't forget that with the Miiverse, things would be now tied to your NNID, which means they would have to overhaul how the entire Friend Code system works to accomodate NNID screennames instead.
Hopefully. Would be good for the friends system and Swapnote to be integrated on 3DS.
Just to clarify, me saying "glorified web app" wasn't a slur against Miiverse. I was just under the impression that all they had planned for 3DS was access to Miiverse via the existing web browser, rather than an actual OS level app.