I use Scrivener to write formally and Ulysses to gather ideas. I have a big issue with Ulysses not being able to change its storage location (in a fully featured way,) and that is almost a deal breaker for me. I like to keep all my writing materials backed up to Dropbox in the case of critical failure.
I think the Windows version of Scrivener is far inferior to the Mac version, and that may be a consideration for you. I’ve never found an application that is as good at taking your drafts and rendering it to a Kindle file and reading the work in that format is fairly critical to my process.