The main problem with the season finale is that it was not a season finale, it was a Season Six first episode - and a confused, mixed one (operation mixed tape in action), by the way, with lots of characters acting out of character (Snow and Emma, mainly, and lots of deus ex machine solutions). Season Five of Once Upon a Time half baked-ly ended on 8th of May and as a season finale 5 x 21 did not give proper closure to the arcs it opened during its exhaustive run. It was a great run with beautiful and meaningful moments, in many aspects, specially because it established an important and definite character development for its central couple: Emma Swan and Killian Jones.
However, exactly because it has moved forward those characters so much, by means of an emotionally extenuating process for both characters (and the audience as well), ending their arc with a single “I love you” and a kiss with a wedding dress in the background is beyond amateurism in terms of narrative development - it is just teasing. When a writer abuses his/her right of teasing the reader, he/she runs the risk of loosing the reader, who will simply give up, close the book and return it to the shelf. As Emma would say, this is not enough for me and, I believe, for Emma and Killian as well. They deserved more, it is completely unrealistic to not give them, after all they have been through, a more mature and grounded closure to their arc. The audience, that suffered their angst together with them, deserved more. I call what they have done abuse of the audience’s and of the characters’ patience. My tolerance has limits, I think they have basically reached it, to be quite honest and I’m afraid this kind of sentiment will be reflected in a trend of lowering on the show ratings as it progresses.
Furthermore, they opened and did not close - and it doesn’t look like they will, arcs that are relevant to the overall story consistency and they just look like will stay forever hanging in the ether of unfinished writing business.
There is huge list of main issues left unanswered - I would call them the primary ones, but there are also secondary ones waving as lost flags in an abandoned ship. @thisisevenharderthannamingablog has listed them here (balance), here (plot lines) and here (structural), I recommend a read of these metas.