I haven't had any syncing issues, but I've had a hell of a time with Evernote insisting on formatting my notes and changing characters even when I make the note Plain Text.
A lot of what I use(d) Evernote for was shell snippets and other bits of code, and having it mangle my quotes into other characters, and randomly insert newlines was a bit of a nightmare.
Thanks to this thread I've found nvALT and I'm really loving it so far.