So... I ditched using the CPP. For now at least.
On one hand, using the stylus with my left-hand is much more comfortable... but on the other hand, stand is pretty damn useful/comfortable and it doesn't hold the 3DS if it has the CPP on it (the 3DS doesn't stick, it just slides right off the holder).
... I haven't really tried using the CPP without the stand much, maybe I'll give it a try again, but damn I'm actually getting comfortable with right-handed controls with the stand. Geez, if I can be pretty comfortable with right-handed controls, I can't imagine how comfortable it must be for actual right-handed people!
As for using your thumb, I only tried it for just a second right now as I read your post, but it seems viable for lefties who really can't get used to holding the stylus with your right hand... I'm still using the stylus though.
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