Problem I had (and for which they were taking some well-deserved heat) is that they switched modes to make it more like Mod Organizer without notifying people what was going to happen. When you downloaded the new version thinking it was merely the minor upgrade its numbering suggested, it gave you a choice of uninstalling all your existing mods or migrating, and migrating did not work for most people. At that point, the only option was to uninstall the new version and manually re-install the old version. There is a roll-back option, but it wasn't working for many people, leaving them back at square one. Luckily it did work for me, but I'm not taking the chance that happens again. For Fallout 4 it might be all right - surely they took enough flaming (including death threats!) to not make that same mistake, and you won't have dozens of carefully installed mods and blended patches for them to nuke as with older games.