Merrill all the way. While Morrigan is definitely a competent adversary, Merrill is not the sweet wouldn't hurt a fly innocent people peg her as. She had the will and the skill to actually handle that blighted eluvian without being harmed, and also does eventually manage to get it working again according to word of god. It seems likely that Morrigan's holier than thou attitude would fuck her over, allowing Merril to get the drop on her.
Honestly I think Merrill, because even though she's a bit shy and goofy, she knows what she wants and does anything to achieve her goal. Sure she reminds me of a cute little mouse but don't forget she's a very capable mage, a first to her keeper and has no problem using blood magic. I think Morrigan's downfall will be to underestimate her. Yes Morrigan is also very powerful, she can shapshift and cast hexes, but I don't think it weighs up to what our little daisy can do