I have, and use, both of them. They do very different things, and so you want to pick the right tool for the right job.
Proteus: good tile damage, low direct damage, and 3-hero mana freeze
He’s really good if you’re facing multiple heroes who are scary if they fire (think GM, Guin and Quintus). He doesn’t make the situation better (mana is frozen, not reduced), but he can buy you time. Fire Proteus, then move tiles around to change the board to best advantage, without fear that dumping tiles will make someone fire.
Merlin: decent direct damage, decent tile damage, and 1-hero mana effect
Merlin is best for dealing with one scary target. Unlike Proteus, he actually can improve your situation. If you dump enough tiles into the target to fill its mana bar, it will damage its own team with a slash attack, and empty its mana to boot. That, plus decent attack damage, is very helpful in coping with one strong target among several weaker targets.
Note, also, that Proteus doesn’t stop mana gain from Alby or Onatel. When facing them, Merlin is by far the better choice, since the fill-up they produce can be countered by pushing the enemy mana bar to full.