I was going to reply to the "First paper published" thread, but the forum said I should create a new topic, so...
I've just had a paper accepted for a pretty decent journal. The whole thing was drafted in Manuscripts (beta 1.2.0)
Positives: writing in Manuscripts feels a lot more stress-free than in a word processor. Tables and figures are much easier to handle than in Scrivener, which has truly terrible support for both. Citations were easy enough to handle in combination with Papers3
Negatives: a whole bunch of issues with justification of text, authors all came out as "unknown", and the tables needed to be fixed in Word prior to publication.
Still: accepted without amendments, which indicates that Manuscripts made it much easier not to make mistakes.
Looking forward to the next version!