When does Cole say about Solas being a spirit made flesh? I've just been round with him with me for every bit except the first trip through the eluvian and he never said anything like that. The only time I recall him saying something specific about Solas was when the Qunari priestess said she was going to kill him and Cole objected that he was a good wolf. I wanted to yell at him that all those skeletons lying around in the library were people who got stranded by Fen'Harel and starved to death, just like the original Cole. Cole apparently seems to have a good idea of all the suffering that is coming but instead of trying to help stop it is just going to turn up to offer "comfort" when it does, which is going to be little consolation to people dying horribly in a world of chaotic flames.
Also where did you read that the forgotten ones were elves who shed their bodies and became demons? I thought the codex said they were simply banished by the Evnauris without indicating exactly what they were. They could have been spirits since the elves could interact freely with them.
I think it makes little difference whether Flemeth took over Solas or he absorbed Mythal and now controls her. The fact is that his plan seems to be to kill millions of innocent people just to try and restore what he destroyed, also resulting in the death of likely millions of people (or at least many thousands).
As for the Well, the oddest thing for me was when he asked me what I was going to do with it when I hadn't even drunk from the thing. When I suggested we shouldn't count our chickens until Cory was out of the way, I got "Solas Disapproves". Actually Morrigan had already told me she was planning on joining the Warden with their son, so I had already assumed that the Well was something I would no longer control. It was noticeable that even before his meeting with Flemeth he would pump you for information whilst revealing very little himself. Every time he let something slip and you attempted to find out more, he would either change the subject or you'd simply get another disapproval (or both). Looking back on it, his actions all the way through fitted perfectly with what he tells you in Trespasser, so whatever plan he is pursuing, he was doing it before the meeting.
I think Flemeth expected him to come because of what happened to his orb, which she knew about. She knew he would be seeking an alternative power so he could continue to pursue his plans. Presumably if our fight with Cory had not drained the orb and cracked it, two years down the line there would be no Inquisitor, Inquisition or anyone else because he would have proceeded with his plan already. I think Flemeth has a contingency plan, involving Morrigan but also required her to surrender to Solas so that ultimately having Mythal inside him will prevent his plan coming to fruition. The reckoning she spoke of was actually with Fen'Harel. Mythal was a protector, who cared for her people and at the core of her being I don't think that has changed. However, she acknowledged my Dalish Inquisitor as one of the People and she also did the same to Merrill, which is why she will stop Solas from destroying them along with everyone else.