Why would it be Merrill? That's clearly a scene for designated Flemeth successor Morrigan.
Also, I think it's not clear when Bioware said half if they meant half in the sense they stopped in the middle or half in the sense that they cut out half the content that they would have had been middle and end. I am however partial to your theory.
The role of guide to ancient elven knowledge and eluvians fits better for Merrill than Morrigan to me. Her character arc can be considered complete in the base game, but there is no real resolution and it feels unfinished to me. Granted, both have been interested in eluvians since their introductions and now that we know Mythal's identity Morrigan's connection to the ancient world makes more sense.
But in a meta way, I think it's far more likely this role would have been given to an existing companion rather than hire Claudia Black for a DLC appearance, especially if she was already going to be in DAI anyway. The way I'm thinking, the Mage-Templar war would have been resolved in DLC but the Orlesian civil war would wait until DAI, so Morrigan would still be in Celene's court at the time.
Kirkwall was so limited in space I doubt an Exalted March storyline would have impressed me.
I imagine it would have occurred outside of Kirkwall, as Legacy and MotA did. It would begin after a Hawke who sided with the mages has abandoned Kirkwall, or after a Hawke who sided with the templars is either taking temporary leave of the viscount throne to try to stop the Exalted March, or has been kicked out by the templars as we see in DAI.
Ostensibly the whole reason Hawke disappeared after DA2 was to try to divert the Exalted March away from Kirkwall and try to hunt down Hawke. Maybe Hawke thought if they could end the fighting between the mages and templars, the EM would be canceled. It would have been interesting if the end of the expansion lead to the Conclave and it still occurred as in DAI. That would make sense for Gaider's comment about an unhappy ending.