Spoiler:
I think that the storyline presented by SG1 is that Merlin was an Atlantian (Ancient) who began to think outside the confined box of the other Atlantians. Perhaps all the time ascended tends to make the mind dull and unimaginative. We saw this same omnipotent action on TNG with the ?Q?. Their interaction with humans gave them something to do; a reason to exist.
So Merlin began to look inward and beyond the omnipotent actions and realize that his fellow ascended beings needed some prodding. We see this in SG1/S10 in bits and pieces with clues littered about.
My theory is this is from his time as the human Janus, ?BEFORE I SLEEP, 1.15?. We saw this man was a thinker out side the box, the example build a time machine against the wishes of his fellow Atlantians, not once but twice at least.
Throw stones, large or small.
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