I was torn between the two cars myself. I ultimately went with the Z because 1)I had a 350z as my previous car and loved it and 2) I was looking at the MR and as I understand it the transmission was not going to be able to handle much modding.
In the end I did get a 7AT Z (which can handle pretty much any bolt on gains). If I do go with a mild FI set up someday, I won't mind shelling out a little more for a
VB job and/or tranny cooler.
Just my 2 cents on the matter.