Let's get this ball rolling!
Here is a list of a few items that we have found during our R80.30 migrations and their status.
Unable to rename or edit comments of an application or cloned application - The reasoning behind why it doesn't let you edit the clones is that you also cannot edit the base application. As they are Check Point defined, there is no option to edit them. A custom application however you can edit. I have an RFE open on this as i can understand not editing a Check Point application that they may update but i think i should have the option to edit a cloned object.
Within Smartlog you can use wildcards for items like an IP address but not for an Origin - You could do 192.168.0.* but can't do customer_x_fw* to see any firewall with the name customer_x_fw. I think this would be helpful when needing to limit the search to one customer and see all of their logs.
cpbackups don't restore the customer CMA/CLM - If using the cpbackup command the customer data is backed up inside the mdsbackup. When a cpbackup is restored using the standard clish method the mdsbackup data is not restored and you are left with an empty /customers folder.