What is the "will of the Lodge?" More importantly, what is the Lodge? The Lodge is all of its members...collectively and individually. The Three Musketeers would recognize what I am saying here. "Unus pro omnibus, omnes pro uno (One for all, all for one)."
This relates directly to the process of electing new members to the Lodge. The creators of the secret, unanimous ballot knew what they were doing and they had it right when they created the system. They knew what some seem to have forgotten, which is that the Lodge is more important than the petitioner. The harmony of the Lodge is more important than the petitioner. Remember, the petitioner is not yet a Brother. He is not yet of the Lodge and he is just a profane who is seeking light. That may sound harsh, but it is the naked truth.
Now, let me speak on the reason the ballot must be unanimous, or nearly unanimous in certain Jurisdictions. The Lodge decides who becomes a member. Not a majority of the Lodge...but THE Lodge (I wish I could emphasize that even more). Remember the phrase, "All for one, one for all." The creators of the ballot system knew that the task of deciding whether or not to admit new members was so important, and had such far-reaching implications, that it could not be left to the few or even to a majority. All of the members have to decide. The Lodge has to decide. Majority rule, though currently the best system for society, creates conflict. Unanimous rule, certainly a utopian concept at this time, creates harmony.
I'll now examine why the ballot is secret. Too easy. Why is your vote for the next President secret? See, even the profane have figured this one out. A voter or a balloter must have complete freedom to go with his conscience. Requiring him to divulge his vote or ballot and/or provide a reason for his decision can influence his action and, thereby, remove some of the freedom that a secret vote or ballot guarantees.
Are good men sometimes denied membership? Of course. It happens. You have to keep in mind, though, that the harmony of the Lodge trumps any perceived "rights" of the petitioner. Masonically speaking, the petitioner has no rights.
The secret, unanimous ballot system is as perfect of a system that I know. I'll say it again. The ballot system is perfect. Any perceived imperfection exists only within the man that holds the little white and black balls between his fingers. Changing an already perfect system will not fix that and may only make it worse. Education is probably the best way to combat any imperfections.