A Romance with Merrill, contrary to prior knowledge, can in fact be attained by playing either a male or female Hawke (although she may receive slightly different Romance Armor depending on Hawke's gender). It will require 50% friendship/rivalry by act 2. Also, like every other romance, flirting is important. Flirt at least once before or during the Questioning Beliefs mid-point relationship conversation in Act 2, which takes place once Mirror Image is done.
You may not get the flirt option if you do not have enough friendship/rivalry. After the Questioning Beliefs has finished, Merrill will visit the Hawke Estate in the evening if her friendship/rivalry level remains at least 50% or more, Flirt with her to initiate the romance and invite her to move in with the PC. Then max out her friendship/rivalry to 100% and do her companion quest and give her both gifts (Halla Carving and Sylvanwood Ring) to complete the romance.
If there is a successful romance, she may end up being kidnapped by Grace in Act 3. Provided she survives everything, she does give Hawke a kiss during the final battle.
In the epilogue Varric will state that due to circumstances after the fight between the Templars and Mages they all had to leave the Champion's side, "Except Merrill of course."