As a professional user, I'm still using GoodNotes, since Penultimate is not yet there. There are 4 important improvements to learn from GoodNotes that would make Penultimate great.
Get a zooming area on the bottom of the screen to comfortably write with the same advance feature like GoodNotes or NoteTakerHD. Turn the page 90 degrees as turning the iPad. Just like GoodNotes or NoteTakerHD. Be able to draw perfect lines, circles, squares and triangles like GoodNotes. Be able to choose your own amount of zoom like GoodNotes or NoteTakerHD.
With those 4 improvements, Penultimate would be the greatest note taker program.