I really like the new setup fee that was introduced in Pro Sites latest release.
I just tested the feature out and it seems like it charges the setup fee regardless of whether or not an existing site has already been charged for it.
For example, my site has free sites disabled, and a Basic and Pro level for $50 and $100 per month respectively. I also have a $199 setup fee.
If a customer signs up for the basic plan they get charged $249 ($50 for 1st month + $199 one-time setup fee).
When they decide they want to upgrade, they get charged $299 ($100 for the monthly fee + $199 one-time setup fee).
Their site would be mostly set up at the time of an upgrade, and they already paid to have it set up once. It doesn't seem right to force a second paid setup...unless I'm missing the idea behind the setup fee? Maybe I'm not thinking about how to use/market it correctly - so don't get me wrong, I'm not opposed to getting paid more!
Perhaps it would be better to create it as an upsell option when choosing a plan. So the customer selects the plan they want and then checks a box next to the one-time setup option if they want it. If they're the DIY type and don't want to have the additional expense then they can opt-out.