This is very coincidental timing for me because I was board at work yesterday and redid my top 100 before even seeing this.
I don't see anything wrong with the way that voting has been done previously. I get that it is boring to see the saw movies over and over again, but there is a reason why those films are mentioned over and over again. I suppose the problem is that with a top 100 list you are going to pick the "greatest" films and many people have similar ideas of what is "great." I'm going to have Citizen Kane, Casablanca, and the Godfather on my lists and so will most others. However, it is disingenuous to have a top 100 list without including those films if you love them.
Maybe the solution is to have a seperate "underloved" list. You would ban anything that appeared on the joint top 100 list and maybe any film that came close. This would shine a spotlight on films that are great, but never makes these lists. Maybe then films like Floating Weeds, Marty, and the Big Heat would get the love that they deserve. Heck, I'm salivating at the idea of finally voting for films like Attack the Gas Station! or Dark City which always missed the cut for me. Finally you would be free of the burden of voting for films that you "have" to and you could start to get creative. It would probably less cohesive than the top 100 list, but it would certainly be interesting.