Just one guy's opinion: Making folder structures or ISOs makes things more complex. Ripping to a container like MKV is more straight forward, more supported, and less complex. Of course when you rip to MKV, you need to figure out the title or titles you want to rip. But you only need to do that once and it's done. MKVs have all of the quality of a folder structure or an ISO. So, unless you love menus, or you like to have every single special feature taking up space in your structures, MKVs don't really have much of a down side.
Just my opinion.
Brian.
