I agree with the OP.
I would like to see more of Flemeth, but only if she's going to be more important to the storyline.
People need to remember, DA:I did not make her Mythal, it made her Mythal's carrier. She's basically just an old powerful mage who is infected with a magical parasite. Nothing interesting there.
Personally, I was hoping they were going to make Flemeth The Formless One, and tied her involvement with the Hero and Champion in to their respective ties to Gaxkang and Xebenkeck. Then have Imshael rejoin the others and have them being the true puppet masters behind the scenes. But no.
Anyway, the plot element that she can make clones of herself and send them to get things done for the main body, I think that's interesting. But this was revealed in DA2, or possibly DA:WH if you read between the lines. Basically, DA:I just shows you who Flemeth works for, and I think that diminished her character.
As for the ending, I think that was just a clone of hers. She was transferring that piece of her back through the eluvian to meet back up with the main host body.
It also appears that Mythal's spirit floated from the Well of Sorrows and then through the eluvian.
So we will see what Mythal's reckoning is, and we will see if Flemeth makes use of the well's compulsion, if it is still placed over the one who drank from the well.