Personally I would go for the Nikon D3200, because it has a significantly higher resolution (24MP instead of 18MP). Provided you can make perfect pictures (using a tripod and good technique), Photoscan will like this extra resolution.
Respectfully, I would completely disagree with this statement. You know, that's what I thought too, until I actually purchased and tested the D3200 against other "similar" offerings by Canon. Don't believe the megapixel hype... because that is what it is.... hype. The Nikon D3200 in both my considerable testing and experience are actually vastly inferior to the lesser megapixel Canon's. Don't believe me, test them side by side for yourself and you will see... both Lee (INFINITE) and I have done just this and the results speak for themselves. I know, this seems counter intuitive but the truth is that until you use these things in production and test under real world conditions specifications put forth by manufacturers and marketing departments mean very little. The proof is in the pudding.
At the end of the day, I'm not trying to change your mind about anything. If you like using the Nikon D3200's more power to you. I have a hybrid rig myself which consists of Nikons and Canon's so I have no axe to grind and I'm not being a fanboy. I only mention this in the hope that I might save you some trouble and perhaps money.
Something else that you should also consider is the cost differential between Nikon and Canon external power supplies. The cost of Nikon power supplies for the D3200 is not trivial and if you have a lot of them, it really adds up fast. While you can find good deals on Canon power supplies the same isn't true for the Nikon's.
Good luck and best wishes in whatever decisions you make.
Cheers,
MC