Just took over Paper Mario on my list of excitment!
Yup, this sounds about right - I think they've started to nail the right effect now; not sure how but not had a problem on more recent games.
It may be more do to with getting a decent 3D effect.
Dark scenes don't play well in 3D and too much light and shade would mean more 3D crosstalk.
Zelda 3DS was really quite bad for it but Kid Icarus seemed to nail it and I don't think I had any cross effect unless I was up at 3AM and my eyes were falling asleep!