Personally I think Emma will make her decision before the end of season three
Oh, I agree, only I think Emma won’t be ready for Neal until close to the end of S3. I think S1 started off in a very similar way, with Emma not being ready to believe in fairytales, and it ended with Emma fulfilling her destiny as the savior. Now we have Emma once again saying she’s not sure she’s ready to explore her relationship with Neal, but if S3 parallels S1, then by 3×22 , I’m thinking Emma will catch up to Neal in being ready for their happy ending. And then S4 will be about Neal and Emma finding their Tallahassee together. Here is a GIF set which shows this parallel between the pilot and 3×10.
We all know that in the end, Emma has a way of getting to where she needs to be. When S1 started she was no where near ready to being the Savior, but by season’s end she was. Likewise, S2 started with Emma having a lot of trust issues, both from having been abandoned by her parents, but also Neal. Yet, S2 ended with Emma saying she loves Neal, that she realized it the instant she ran into Neal. Tamara was just a wall which could be moved, just as I believe Hook will only be a temporary obstacle. S3 started with Neal awakening from a near-death experience with renewed clarity and with him fighting to get back to Emma and Henry, because they’re all he has. Neal’s goal is to be there for them. Yet, there is the new curse coming, much like there was this curse that Emma had to break in S1. While Emma isn’t sure she ready, I’m all but certain that by the end of S3, Emma will have caught up emotionally to where Neal is at. Part of being right for one another means being ready at the same time, and both of them will then be ready to explore their relationship going forward.
"That’s how you know you’ve really got a home. When you leave it, there’s this feeling that you can’t shake. You just miss it." Neal Cassidy