"Has the American view of religion due to the dominance of Christianity taken anything from practicing Aikido? "
As always when you try to remove the roots or original motive of something to suite a larger group opposed to it's motive's, it's meaning is lost
"Along the same lines, does the large-scale commercialization of martial arts detract from Aikido training? "
Watering something down always makes it more apealing to a larger group scince they can apply their own motives to it. The question is if we want to dissect and modify an art with it's roots in a ancient foreign culture just because it takes some effort to grasp the cultural context.
"Do you ever wish that your dojo was a little less religiously sterile, or do you prefer that it be more neutral? "
I've learned to live with the fact that the majority of people (sweden too) do not want any spiritual or religious content in anything scince that means they'll have to ADAPT! to foreign concepts... *shivering*. They just want to come to class and "wrestle in white pyjamases" twice a week, go home and leave their "recreation" behind.
"Is it ok to traditionalize shinto religious practices so that they are acceptible to Americans, or would it be better to drop them entirely since their meaning is no longer present in many dojo?"
Given that you use shinto elements as part of Aikido ritual i think you should either respect them and carry them out in a faithful manner or not do them at all. We might not think that shinto should affect our training and if that is the case we could atleast have enough respect towards practicing shintoists that we don't try to make our own home-made, modified version just to fit our personal whim's.
Aikido is a japanese art created in a japanese enviroment. That's not an oppinion but a fact. Take it or leave it.