To me the biggest bug is one I think every one already knows about.
When using the pen, things can really get distorted if you try to draw off the edge of the screen.
Can this be fixed, or should we plan to live with it?

Yeah, it's one thing not allowing sprites to go off-screen, but another to make lots of extra work for those trying to use the pen to draw things that can partly go off-screen…

Take a look at this project for custom pen blocks you can use instead that overcome the limitation (part of a series in a studio to build a 3D engine):

http://beta.scratch.mit.edu/projects/10094319/

Enjoy!