The main problem is that all the grid-lines on the 9x9 grid are the same width instead of using thicker lines around each 3x3 group.

Other minor problems include:

1. The blue border around the currently selected square partially obscures the text in the notes.  (The Gnome2 version changed the foreground and background colors of the whole square, so none of it was obscured by a colored internal border.)

2. The size of the note text entry box seems excessive and covers several squares (depending on the window size and font size), so you can't refer to the contents of several squares while entering the note.  (The Gnome2 version kept the text entry box within the bounds of the square to which it applied, so you could see all the other squares while typing the note.)

All the above detract from the playability compared to the Gnome2 version, IMHO.