This isn't an easy problem to solve because all writers are idiosyncratic. :)
I largely moved from Scrivener to Ulysses, which is Markdown-centric, maintains feature parity between the Mac app and the iPad/iPhone apps, and has pretty rock-solid syncing. But it doesn't have Scrivener's "import anything into your project" approach to saving research material -- it doesn't have anything I would describe as "asset management," period, although documents can embed images -- and is, if anything, even more opinionated about How To Do Things, and you may not share its opinions. And, it's Apple-only, which could be a dealbreaker depending on your ecosystem.
