Actually, I had never used Flipnote Studio before, this was the first time (and maybe the last.) On the other hand I had already created other full color animations using the combo Retas/Photoshop/After Effects/Premiere. I used flipnote studio intensively for 3 days and I think this is a good tool for creating short animations. The problem is you can't create complicated montage unless you know where you're going when it comes to the order of the scenes/cuts. I drew a storyboard on paper before doing this on flipnote because I knew it would be troublesome to change the order of scene one by one afterwards.
In fact, I think this app is rather made to create cool animation sequence with few scenes (hence the term flipnote) rather than complicated stories with lots of cuts. The drawing tools are very simple and easy to use : pen, rubber, and a brush to add different kind of tones like in mangas, the lasso. You can draw on 2 layers and add a soundtrack and 3 sounds (which I think is very limited and not very convenient but you can't ask too much for a free program)
In the end, it's always the same : the tool is great but what really counts is the talent and the patience of the user. Actually, I still prefer to draw on paper for animation but this is a good tool to try new things rather quickly. On flipnote hatena, choose Japan and you can see some great flipnotes.