There are three instances to the puzzles that are itching my head where I 'sense' contradictions (or inconclusiveness) but cannot fully explain what, how, or why so I'll do my best.
End of questions
Now here I am thinking and theorizing ... Merlin might not have been developing a weapon whatsoever. Merlin might have contributed to the origination/creation of the Ori. Consider the title of the final episode of season 10 'Family Ties'. The Ori may have been an abandoned offspring of the Ancients and are returning for retribution (similarly to how we now see how the Wraith and Asurans are coming back for revenge on their creators).
Merlin was considered an outcast for his research. Morgan LaFey (over time) began to question the codes and conduct of the Ascended. Even Morgan LaFey herself said there was a small group of ascended resistance, but not enough. I suppose even as an Ascended being, there's no escaping politics.
And so, everything seems to be coming back in a circle. What began with the Ancients will end with the Ancients, as what the Ancients began will also end with the Ancients.
Ancients created problems they couldn't control (i.e. wraith infestation, mutation, war), ignored the consequences (i.e. Project Arcturus, Window of Opportunity), tried to shove the problems under the carpet (i.e. annihilating the Pegasus replicator colony), and now many of the problems they chose to ignore are coming back to haunt them.
In conclusion, I'm predicting that Merlins' weapon to fight the ascended Ancients are indeed the Ori.