I love this conversation. It proves that no two experiences are exactly the same.
If I may devil's advocate for both sides (security deposit vs move-in-fee);
I am a numbers guy so I love what you have illustrated @Jason Albasha. It can make sense to secure 1/3 of the money instead of returning ALL of the security deposit. A couple sayings come to mind: "A bird in the hand is worth two in the bush" and "A dollar today is worth more than a dollar tomorrow". Having that move-in fee and being able to put it to work for you from day one is a nice option to have.
On the other hand, we shouldn't just downplay someones proven record. @John Warren seems to be saying that from, his experience, his renters have shown that having a security deposit looming over them has motivated them to leave the unit to a level that is required. I wouldn't say that he is "assuming tenants will do less damage". I would say his tenant base have shown that they do care about the possible $1500 being lost if they don't leave the place spot less. I would assume most people that are only paying $1000 for rent aren't the kind of folks to want $1500 to slip away from them (no matter whether they are good or bad tenants).
It would be good to hear from others with experience on either side. I wonder how often someone gets a destroyed unit when the tenant leaves and there is not security deposit to cover anything. I doubt the $500 move-in fee would cover much in that scenario. But I may be wrong.
I personally have one unit with a security deposit in La Grange and a house in Brookfield being rented where I did a move-in fee. I know the people in the Brookfield house so I am confident we would have a decent experience on a move out. I have mixed feelings with the security deposit unit. On one hand I do like having that money to fall back on if anything comes up. But with all the laws and rules about how much you have to return with interest and all, it makes it less comfortable for me to hold deposits.