I've tried getting into around with pd a couple of times before, this is my first concerted time.  I've worked with a bunch of flow-charty programming environments in the past (Unreal Engine's kismet is the slickest I've come across - http://odedge.com/forums/ut3_kismet_04.jpg ) - pure data is taking a bit of getting used to (most of this is due to the fact that it does special things, some things feel a bit more avoidable, other things feel frivolously subjective :P ).  Here're some of the things that stuck out for me (some might be due to ignorance on my part, I'd love to have things cleared up :) ):

1 - Inlets/outlets too small for me to accurately click on (touchpad) - checking on pd-dev, they can be visually reskinned, but their actual clickable size can't be changed.  [ so I guess this one has been responded to, but might as well repeat it ]
2 - If I have an object selected (that's to say pressing buttons to edit text in it) I can't find any key-combination that will delete it - I have to deselect it, then press the mouse down on it, then, while holding the mouse button down, press backspace? (this is an uncomfortable manipulation on a laptop w/ touchpad) - on OSX at least, a shortcut like cmd+backspace would be quite idiomatic for this.
3 - I can drag lines from outlets to inlets, but not from inlets to outlets.
4 - is there a shortcut for deleting connections?  something like ctrl+click would save me a lot of time.
5 - is there a way to type numbers directly into a number box? clicking+dragging, or pumping them in via a message, doesn't feel good to me.
6 - shortcut for opening help of selected item would be...convenient for me

I'm still working through the tutorials, and am enjoying the experience overall :)