it might also be useful to have a very subtle background grid drawn on the canvas at certain intervals to help patch organization. Quartz Composer has this, as does Max 5 (not saying you HAVE to have it, but it might be a nice addition.
I look at this as the equivalent of properly indented code; a feature I'd really appreciate is the equivalent of auto-indenting since I obsessively line up my Pd patches.
Secondly, maybe consider making message boxes, object boxes and subpatch boxes each a different color? I'd consider this the equivalent of syntax highlighting, and though I'm sure choice of default colors will be contentious, I think it would be a boon for busy patches (especially the subpatch/objectbox differentiation; I am always searching for subpatches).
And finally, it pains me that much of this work we're discussing has already been done by Mathieu and Chun : (! I have a dream, where DD and PD and PD-E are one.
Cheers Luke